bioroebe 0.12.24 → 0.13.32

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Files changed (503) hide show
  1. checksums.yaml +4 -4
  2. data/LICENSE.md +7 -8
  3. data/README.md +566 -354
  4. data/bin/all_positions_of_this_nucleotide +1 -1
  5. data/bin/aminoacid_frequencies +1 -1
  6. data/bin/automatically_rename_this_fasta_file +1 -1
  7. data/bin/base_composition +1 -1
  8. data/bin/batch_create_windows_executables +1 -1
  9. data/bin/bioroebe +12 -1
  10. data/bin/bioroebe_cat +7 -0
  11. data/bin/calculate_exponential_growth +7 -0
  12. data/bin/calculate_n50_value +1 -1
  13. data/bin/calculate_the_frequencies_of_this_species +7 -0
  14. data/bin/chunked_display +1 -1
  15. data/bin/codon_frequency +1 -1
  16. data/bin/codon_to_aminoacid +1 -1
  17. data/bin/colourize_this_fasta_sequence +1 -1
  18. data/bin/complementary_dna_strand +1 -1
  19. data/bin/complementary_rna_strand +1 -1
  20. data/bin/consensus_sequence +1 -1
  21. data/bin/dna_to_rna +1 -1
  22. data/bin/downcase_chunked_display +1 -1
  23. data/bin/download_this_pdb +1 -1
  24. data/bin/fasta_index +1 -1
  25. data/bin/fetch_data_from_uniprot +1 -1
  26. data/bin/filter_away_invalid_nucleotides +1 -1
  27. data/bin/find_substring +1 -1
  28. data/bin/input_as_dna +1 -1
  29. data/bin/is_palindrome +1 -1
  30. data/bin/leading_five_prime +1 -1
  31. data/bin/longest_ORF +1 -1
  32. data/bin/longest_substring +1 -1
  33. data/bin/open_reading_frames +1 -1
  34. data/bin/partner_nucleotide +1 -1
  35. data/bin/plain_palindrome +1 -1
  36. data/bin/random_dna_sequence +1 -1
  37. data/bin/random_sequence +1 -1
  38. data/bin/raw_hamming_distance +1 -1
  39. data/bin/return_longest_substring_via_LCS_algorithm +1 -1
  40. data/bin/reverse_sequence +1 -1
  41. data/bin/short_aminoacid_letter_from_long_aminoacid_name +1 -1
  42. data/bin/show_atomic_composition +1 -1
  43. data/bin/show_fasta_header +1 -1
  44. data/bin/show_nucleotide_sequence +1 -1
  45. data/bin/show_this_dna_sequence +1 -1
  46. data/bin/show_time_now +7 -0
  47. data/bin/sort_aminoacid_based_on_its_hydrophobicity +1 -1
  48. data/bin/strict_filter_away_invalid_aminoacids +1 -1
  49. data/{lib/bioroebe/base/reset.rb → bin/three_delimiter} +9 -6
  50. data/bin/three_to_one +1 -1
  51. data/bin/to_rna +1 -1
  52. data/bin/trailing_three_prime +1 -1
  53. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +1 -1
  54. data/bioroebe.gemspec +6 -7
  55. data/doc/README.gen +534 -322
  56. data/doc/blosum/blosum.md +4 -0
  57. data/doc/compatibility/BIO_PHP.md +20 -18
  58. data/doc/compatibility/README.md +2 -3
  59. data/doc/compatibility/emboss.md +5 -3
  60. data/doc/{extensive_usage_example.md → extensive_usage_example/extensive_usage_example.md} +4 -2
  61. data/doc/{instructions_for_the_taxonomy_subproject.md → instructions_for_the_taxonomy_subproject/instructions_for_the_taxonomy_subproject.md} +36 -33
  62. data/doc/{legacy_paths.md → legacy_paths/legacy_paths.md} +3 -3
  63. data/doc/statistics/statistics.md +12 -10
  64. data/doc/todo/bioroebe_GUI_todo.md +6 -1
  65. data/doc/todo/bioroebe_java_todo.md +3 -2
  66. data/doc/todo/bioroebe_todo.md +352 -310
  67. data/doc/{using_biomart.md → using_biomart/using_biomart.md} +7 -3
  68. data/lib/bioroebe/abstract/features.rb +0 -0
  69. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -1
  70. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +3 -1
  71. data/lib/bioroebe/aminoacids/codon_percentage.rb +18 -10
  72. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +5 -2
  73. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +90 -64
  74. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -3
  75. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +2 -2
  76. data/lib/bioroebe/annotations/create_annotation_format.rb +2 -2
  77. data/lib/bioroebe/base/base.rb +101 -6
  78. data/lib/bioroebe/base/base_module/base_module.rb +9 -1
  79. data/lib/bioroebe/base/colours.rb +3 -0
  80. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +80 -44
  81. data/lib/bioroebe/base/commandline_application/README.md +1 -1
  82. data/lib/bioroebe/base/commandline_application/commandline_application.rb +663 -22
  83. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +2 -1
  84. data/lib/bioroebe/base/infer_the_namespace_module/infer_the_namespace_module.rb +37 -0
  85. data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +1 -6
  86. data/lib/bioroebe/base/prototype/prototype.rb +155 -14
  87. data/lib/bioroebe/biomart/attribute.rb +1 -1
  88. data/lib/bioroebe/biomart/biomart.rb +8 -9
  89. data/lib/bioroebe/biomart/server.rb +1 -1
  90. data/lib/bioroebe/blosum/blosum.rb +2 -2
  91. data/lib/bioroebe/calculate/calculate_blosum_score.rb +5 -3
  92. data/lib/bioroebe/calculate/calculate_gc_content.rb +1 -1
  93. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +5 -3
  94. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +2 -10
  95. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +6 -15
  96. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +4 -2
  97. data/lib/bioroebe/cell/cell.rb +3 -2
  98. data/lib/bioroebe/cell/specialized_cells/B_cell.rb +60 -0
  99. data/lib/bioroebe/cell/specialized_cells/Macrophage.rb +60 -0
  100. data/lib/bioroebe/cell/specialized_cells/README.md +5 -0
  101. data/lib/bioroebe/cell/specialized_cells/T_cell.rb +60 -0
  102. data/lib/bioroebe/cleave_and_digest/cleave.rb +3 -1
  103. data/lib/bioroebe/cleave_and_digest/digestion.rb +1 -1
  104. data/lib/bioroebe/codon_tables/frequencies/10090_Mus_musculus.yml +93 -0
  105. data/lib/bioroebe/codon_tables/frequencies/107243_Thlaspi_caerulescens.yml +72 -0
  106. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -2
  107. data/lib/bioroebe/codons/codon_table.rb +10 -2
  108. data/lib/bioroebe/codons/codons.rb +3 -3
  109. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +18 -15
  110. data/lib/bioroebe/codons/determine_optimal_codons.rb +1 -1
  111. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +4 -2
  112. data/lib/bioroebe/codons/show_codon_tables.rb +1 -1
  113. data/lib/bioroebe/codons/show_codon_usage.rb +1 -2
  114. data/lib/bioroebe/codons/show_this_codon_table.rb +2 -2
  115. data/lib/bioroebe/codons/start_codons.rb +7 -3
  116. data/lib/bioroebe/colours/colour_schemes/README.md +1 -1
  117. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +3 -3
  118. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +3 -3
  119. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +4 -3
  120. data/lib/bioroebe/colours/colour_schemes/helix.rb +3 -1
  121. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +3 -1
  122. data/lib/bioroebe/colours/colour_schemes/score.rb +13 -2
  123. data/lib/bioroebe/colours/colour_schemes/strand.rb +3 -1
  124. data/lib/bioroebe/colours/colour_schemes/turn.rb +3 -1
  125. data/lib/bioroebe/colours/colour_schemes/zappo.rb +1 -1
  126. data/lib/bioroebe/{toplevel_methods/colourize_related_methods.rb → colours/colourize_related_code.rb} +1 -3
  127. data/lib/bioroebe/colours/colourize_sequence.rb +3 -1
  128. data/lib/bioroebe/colours/colours.rb +172 -15
  129. data/lib/bioroebe/configuration/configuration.rb +1 -1
  130. data/lib/bioroebe/constants/GUIs.rb +2 -2
  131. data/lib/bioroebe/constants/constants.rb +1349 -0
  132. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +8 -13
  133. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +62 -16
  134. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +11 -10
  135. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +1 -1
  136. data/lib/bioroebe/count/count_at.rb +2 -1
  137. data/lib/bioroebe/databases/download_taxonomy_database.rb +1 -1
  138. data/lib/bioroebe/dotplots/advanced_dotplot.rb +2 -2
  139. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +2 -2
  140. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +2 -2
  141. data/lib/bioroebe/electron_microscopy/flipy.rb +2 -2
  142. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +3 -11
  143. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +15 -15
  144. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +6 -6
  145. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +2 -2
  146. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +1 -1
  147. data/lib/bioroebe/enzymes/restriction_enzyme.rb +1 -1
  148. data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +4 -3
  149. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +1 -1
  150. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +4 -3
  151. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +3 -3
  152. data/lib/bioroebe/ext/main.cpp +0 -1
  153. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +3 -3
  154. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +1 -1
  155. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +1 -1
  156. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +11 -17
  157. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -1
  158. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +1 -1
  159. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +1 -1
  160. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +1 -1
  161. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +37 -11
  162. data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +2 -2
  163. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +1 -1
  164. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +5 -13
  165. data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +1 -1
  166. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -1
  167. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +3 -6
  168. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +3 -3
  169. data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +20 -11
  170. data/lib/bioroebe/genome/genome.rb +1 -1
  171. data/lib/bioroebe/genomes/genome_pattern.rb +17 -16
  172. data/lib/bioroebe/genomes/genome_retriever.rb +4 -2
  173. data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +10 -13
  174. data/lib/bioroebe/gui/universal_widgets/alignment/alignment.rb +557 -0
  175. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/aminoacid_composition.rb +498 -198
  176. data/lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb +665 -0
  177. data/lib/bioroebe/gui/universal_widgets/blosum_matrix_viewer/blosum_matrix_viewer.rb +329 -0
  178. data/lib/bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +423 -0
  179. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/controller/controller.rb +170 -118
  180. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +277 -215
  181. data/lib/bioroebe/gui/{shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb → universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb} +297 -107
  182. data/lib/bioroebe/gui/universal_widgets/fasta_table_widget/fasta_table_widget.rb +643 -0
  183. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/format_converter/format_converter.rb +236 -164
  184. data/lib/bioroebe/gui/universal_widgets/gene/gene.rb +278 -0
  185. data/lib/bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb +646 -0
  186. data/lib/bioroebe/gui/{shared_code/levensthein_distance/levensthein_distance_module.rb → universal_widgets/levensthein_distance/levensthein_distance.rb} +313 -88
  187. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/nucleotide_analyser/nucleotide_analyser.rb +281 -189
  188. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/parse_pdb_file/parse_pdb_file.rb +265 -149
  189. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/primer_design_widget/primer_design_widget.rb +337 -263
  190. data/lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb +408 -0
  191. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/random_sequence/random_sequence.rb +245 -187
  192. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.rb +207 -137
  193. data/lib/bioroebe/gui/universal_widgets/shell/shell.rb +288 -0
  194. data/lib/bioroebe/gui/{gtk3/show_codon_table/misc.rb → universal_widgets/show_codon_table/show_codon_table.rb} +290 -110
  195. data/lib/bioroebe/gui/{shared_code/show_codon_usage/show_codon_usage_module.rb → universal_widgets/show_codon_usage/show_codon_usage.rb} +228 -47
  196. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/sizeseq/sizeseq.rb +151 -69
  197. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/three_to_one/three_to_one.rb +190 -127
  198. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.rb +211 -152
  199. data/lib/bioroebe/images/images.html +953 -1170
  200. data/lib/bioroebe/images/misc/README.md +6 -0
  201. data/lib/bioroebe/images/misc/activation.avif +0 -0
  202. data/lib/bioroebe/images/misc/inhibition.avif +0 -0
  203. data/lib/bioroebe/images/misc/small_virus_logo.avif +0 -0
  204. data/lib/bioroebe/{constants/base_directory.rb → log_directory/log_directory.rb} +79 -59
  205. data/lib/bioroebe/matplotlib/matplotlib_generator.rb +1 -1
  206. data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +1 -1
  207. data/lib/bioroebe/misc/ruler.rb +5 -5
  208. data/lib/bioroebe/misc/useful_formulas.rb +3 -3
  209. data/lib/bioroebe/ncbi/efetch.rb +3 -4
  210. data/lib/bioroebe/ngs/phred_quality_score_table.rb +3 -3
  211. data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +3 -6
  212. data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +3 -3
  213. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +6 -10
  214. data/lib/bioroebe/nucleotides/{show_nucleotide_sequence.rb → show_nucleotide_sequence/show_nucleotide_sequence.rb} +377 -255
  215. data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +1 -1
  216. data/lib/bioroebe/palindromes/palindrome_finder.rb +1 -1
  217. data/lib/bioroebe/palindromes/palindrome_generator.rb +2 -10
  218. data/lib/bioroebe/parsers/biolang_parser.rb +1 -1
  219. data/lib/bioroebe/parsers/blosum_parser.rb +14 -19
  220. data/lib/bioroebe/parsers/genbank_parser.rb +2 -6
  221. data/lib/bioroebe/parsers/gff.rb +9 -9
  222. data/lib/bioroebe/parsers/parse_embl.rb +2 -6
  223. data/lib/bioroebe/parsers/stride_parser.rb +4 -12
  224. data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +2 -2
  225. data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +6 -3
  226. data/lib/bioroebe/patterns/profile_pattern.rb +2 -2
  227. data/lib/bioroebe/patterns/rgg_scanner.rb +4 -2
  228. data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/alpha_helix.rb +2 -2
  229. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/download_this_pdb.rb +2 -3
  230. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/fetch_fasta_sequence_from_pdb.rb +4 -4
  231. data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/helical_wheel.rb +2 -2
  232. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_mmCIF_file.rb +1 -1
  233. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_pdb_file.rb +3 -3
  234. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/report_secondary_structures_from_this_pdb_file.rb +3 -3
  235. data/lib/bioroebe/project/project.rb +3 -1
  236. data/lib/bioroebe/raw_sequence/README.md +8 -8
  237. data/lib/bioroebe/raw_sequence/raw_sequence.rb +11 -2
  238. data/lib/bioroebe/regexes/regexes.rb +1 -2
  239. data/lib/bioroebe/requires/commandline_application.rb +3 -1
  240. data/lib/bioroebe/requires/require_all_pdb_files.rb +1 -1
  241. data/lib/bioroebe/requires/require_all_taxonomy_files.rb +1 -1
  242. data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +10 -0
  243. data/lib/bioroebe/requires/require_colours.rb +1 -1
  244. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +5 -7
  245. data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +1 -1
  246. data/lib/bioroebe/requires/require_the_constants.rb +2 -14
  247. data/lib/bioroebe/requires/require_yaml.rb +7 -5
  248. data/lib/bioroebe/sequence/alignment.rb +1 -1
  249. data/lib/bioroebe/sequence/dna.rb +4 -2
  250. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +22 -8
  251. data/lib/bioroebe/sequence/protein.rb +2 -2
  252. data/lib/bioroebe/sequence/reverse_complement.rb +3 -3
  253. data/lib/bioroebe/sequence/rna.rb +9 -8
  254. data/lib/bioroebe/sequence/sequence.rb +3 -3
  255. data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +0 -0
  256. data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +0 -0
  257. data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +0 -0
  258. data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -1
  259. data/lib/bioroebe/shell/help/class.rb +68 -19
  260. data/lib/bioroebe/shell/menu.rb +5244 -5322
  261. data/lib/bioroebe/shell/{readline/readline.rb → readline.rb} +1 -3
  262. data/lib/bioroebe/shell/shell.rb +11240 -453
  263. data/lib/bioroebe/siRNA/siRNA.rb +3 -3
  264. data/lib/bioroebe/{gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb → sinatra/sinatra_interface.rb} +28 -19
  265. data/lib/bioroebe/{www/sinatra/sinatra.rb → sinatra/sinatra_wrapper.rb} +731 -754
  266. data/lib/bioroebe/string_matching/find_longest_substring.rb +2 -10
  267. data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +4 -14
  268. data/lib/bioroebe/string_matching/hamming_distance.rb +17 -16
  269. data/lib/bioroebe/string_matching/levensthein.rb +5 -17
  270. data/lib/bioroebe/string_matching/simple_string_comparer.rb +48 -4
  271. data/lib/bioroebe/string_matching/smith_waterman.rb +11 -6
  272. data/lib/bioroebe/svg/glyph.rb +4 -1
  273. data/lib/bioroebe/svg/mini_feature.rb +1 -1
  274. data/lib/bioroebe/svg/page.rb +18 -7
  275. data/lib/bioroebe/svg/svgee.rb +22 -13
  276. data/lib/bioroebe/svg/track.rb +20 -4
  277. data/lib/bioroebe/taxonomy/chart.rb +2 -2
  278. data/lib/bioroebe/taxonomy/class_methods.rb +5 -6
  279. data/lib/bioroebe/taxonomy/constants.rb +1 -1
  280. data/lib/bioroebe/taxonomy/info/info.rb +1 -1
  281. data/lib/bioroebe/taxonomy/info/is_dna.rb +1 -1
  282. data/lib/bioroebe/taxonomy/interactive.rb +5 -4
  283. data/lib/bioroebe/taxonomy/menu.rb +1 -1
  284. data/lib/bioroebe/taxonomy/node.rb +1 -1
  285. data/lib/bioroebe/taxonomy/parse_fasta.rb +4 -2
  286. data/lib/bioroebe/taxonomy/shared.rb +5 -4
  287. data/lib/bioroebe/taxonomy/taxonomy.rb +2 -4
  288. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +3 -45
  289. data/lib/bioroebe/toplevel_methods/{is_on_roebe.rb → roebe.rb} +1 -11
  290. data/lib/bioroebe/toplevel_methods/taxonomy.rb +6 -12
  291. data/lib/bioroebe/toplevel_methods/toplevel_methods.rb +5607 -0
  292. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +4 -3
  293. data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +2 -2
  294. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +16 -9
  295. data/lib/bioroebe/utility_scripts/compacter/compacter.rb +4 -2
  296. data/lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb +119 -0
  297. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +11 -9
  298. data/lib/bioroebe/utility_scripts/{consensus_sequence.rb → consensus_sequence/consensus_sequence.rb} +13 -4
  299. data/lib/bioroebe/utility_scripts/{create_batch_entrez_file.rb → create_batch_entrez_file/create_batch_entrez_file.rb} +5 -5
  300. data/lib/bioroebe/utility_scripts/{determine_antigenic_areas.rb → determine_antigenic_areas/determine_antigenic_areas.rb} +5 -5
  301. data/lib/bioroebe/utility_scripts/{determine_missing_nucleotides_percentage.rb → determine_missing_nucleotides_percentage/determine_missing_nucleotides_percentage.rb} +16 -15
  302. data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +7 -7
  303. data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +1 -1
  304. data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +2 -0
  305. data/lib/bioroebe/utility_scripts/{dot_alignment.rb → dot_alignment/dot_alignment.rb} +3 -3
  306. data/lib/bioroebe/utility_scripts/{download_files_from_rebase.rb → download_files_from_rebase/download_files_from_rebase.rb} +5 -5
  307. data/lib/bioroebe/utility_scripts/fetch_data_from_uniprot/fetch_data_from_uniprot.rb +269 -0
  308. data/lib/bioroebe/utility_scripts/find_gene.rb +4 -2
  309. data/lib/bioroebe/utility_scripts/{mirror_repeat.rb → mirror_repeat/mirror_repeat.rb} +5 -5
  310. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +3 -3
  311. data/lib/bioroebe/utility_scripts/{parse_taxonomy.rb → parse_taxonomy/parse_taxonomy.rb} +15 -6
  312. data/lib/bioroebe/utility_scripts/{pathways.rb → pathways/pathways.rb} +4 -3
  313. data/lib/bioroebe/utility_scripts/{permutations.rb → permutations/permutations.rb} +3 -3
  314. data/lib/bioroebe/utility_scripts/punnet/punnet.rb +4 -2
  315. data/lib/bioroebe/utility_scripts/{show_this_dna_sequence.rb → show_this_dna_sequence/show_this_dna_sequence.rb} +1 -1
  316. data/lib/bioroebe/utility_scripts/showorf/showorf.rb +406 -10
  317. data/lib/bioroebe/version/version.rb +2 -2
  318. data/lib/bioroebe/viennarna/rnafold_wrapper.rb +5 -13
  319. data/lib/bioroebe/virus/individual_viruses/README.md +15 -0
  320. data/lib/bioroebe/virus/individual_viruses/tobacco_mosaic_virus.rb +40 -0
  321. data/lib/bioroebe/virus/virus.rb +76 -0
  322. data/lib/bioroebe/www/bioroebe.cgi +4 -3
  323. data/lib/bioroebe/www/embeddable_interface.rb +85 -49
  324. data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +6 -6
  325. data/lib/bioroebe/yaml/antisense/antisense.yml +2 -0
  326. data/lib/bioroebe/yaml/blosum/blosum50.yml +6 -0
  327. data/lib/bioroebe/yaml/blosum/blosum90.yml +2 -1
  328. data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +2 -2
  329. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
  330. data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
  331. data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +7 -6
  332. data/lib/bioroebe/yaml/humans/human_chromosomes.yml +3 -3
  333. data/lib/bioroebe/yaml/mRNA/mRNA.yml +1 -5
  334. data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +1 -0
  335. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +2 -1
  336. data/lib/bioroebe/yaml/promoters/35S.yml +3 -1
  337. data/lib/bioroebe/yaml/proteases/proteases.yml +3 -1
  338. data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -1
  339. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +7 -7
  340. data/spec/testing_toplevel_method_editor.rb +1 -1
  341. data/spec/testing_toplevel_method_verbose.rb +1 -1
  342. data/test/testing_dna_to_rna_conversion.rb +1 -1
  343. metadata +127 -235
  344. data/doc/blosum.md +0 -5
  345. data/lib/bioroebe/base/commandline_application/aminoacids.rb +0 -33
  346. data/lib/bioroebe/base/commandline_application/directory.rb +0 -33
  347. data/lib/bioroebe/base/commandline_application/extract.rb +0 -22
  348. data/lib/bioroebe/base/commandline_application/misc.rb +0 -502
  349. data/lib/bioroebe/base/commandline_application/opn.rb +0 -47
  350. data/lib/bioroebe/base/commandline_application/reset.rb +0 -42
  351. data/lib/bioroebe/base/commandline_application/warnings.rb +0 -36
  352. data/lib/bioroebe/base/commandline_application/write_what_into.rb +0 -29
  353. data/lib/bioroebe/base/initialize.rb +0 -18
  354. data/lib/bioroebe/base/misc.rb +0 -129
  355. data/lib/bioroebe/base/namespace.rb +0 -16
  356. data/lib/bioroebe/base/prototype/e_and_ee.rb +0 -24
  357. data/lib/bioroebe/base/prototype/misc.rb +0 -114
  358. data/lib/bioroebe/base/prototype/mkdir.rb +0 -20
  359. data/lib/bioroebe/base/prototype/reset.rb +0 -36
  360. data/lib/bioroebe/colours/misc_colours.rb +0 -80
  361. data/lib/bioroebe/colours/rev.rb +0 -44
  362. data/lib/bioroebe/colours/sdir.rb +0 -21
  363. data/lib/bioroebe/colours/sfancy.rb +0 -21
  364. data/lib/bioroebe/colours/sfile.rb +0 -21
  365. data/lib/bioroebe/colours/simp.rb +0 -21
  366. data/lib/bioroebe/colours/swarn.rb +0 -29
  367. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +0 -147
  368. data/lib/bioroebe/constants/carriage_return.rb +0 -14
  369. data/lib/bioroebe/constants/codon_tables.rb +0 -77
  370. data/lib/bioroebe/constants/database_constants.rb +0 -107
  371. data/lib/bioroebe/constants/files_and_directories.rb +0 -606
  372. data/lib/bioroebe/constants/misc.rb +0 -209
  373. data/lib/bioroebe/constants/newline.rb +0 -14
  374. data/lib/bioroebe/constants/nucleotides.rb +0 -121
  375. data/lib/bioroebe/constants/regex.rb +0 -28
  376. data/lib/bioroebe/constants/roebe.rb +0 -38
  377. data/lib/bioroebe/constants/row_terminator.rb +0 -16
  378. data/lib/bioroebe/constants/tabulator.rb +0 -14
  379. data/lib/bioroebe/constants/unicode.rb +0 -12
  380. data/lib/bioroebe/constants/urls.rb +0 -50
  381. data/lib/bioroebe/gui/gtk +0 -1
  382. data/lib/bioroebe/gui/gtk3/README.md +0 -2
  383. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +0 -306
  384. data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +0 -29
  385. data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -195
  386. data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -105
  387. data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -188
  388. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +0 -322
  389. data/lib/bioroebe/gui/gtk3/gene/gene.rb +0 -181
  390. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +0 -383
  391. data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +0 -174
  392. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +0 -181
  393. data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +0 -101
  394. data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +0 -145
  395. data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +0 -23
  396. data/lib/bioroebe/gui/jruby/alignment/alignment.rb +0 -165
  397. data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +0 -166
  398. data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -82
  399. data/lib/bioroebe/gui/libui/README.md +0 -4
  400. data/lib/bioroebe/gui/libui/alignment/alignment.rb +0 -116
  401. data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -112
  402. data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -60
  403. data/lib/bioroebe/gui/libui/controller/controller.rb +0 -116
  404. data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +0 -161
  405. data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -76
  406. data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +0 -135
  407. data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +0 -118
  408. data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +0 -115
  409. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +0 -190
  410. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +0 -134
  411. data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +0 -89
  412. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +0 -113
  413. data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +0 -102
  414. data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +0 -94
  415. data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +0 -216
  416. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +0 -192
  417. data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +0 -72
  418. data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +0 -206
  419. data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -140
  420. data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +0 -262
  421. data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +0 -243
  422. data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +0 -199
  423. data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +0 -519
  424. data/lib/bioroebe/shell/colours/colours.rb +0 -235
  425. data/lib/bioroebe/shell/help/help.rb +0 -25
  426. data/lib/bioroebe/shell/misc.rb +0 -10227
  427. data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +0 -56
  428. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +0 -722
  429. data/lib/bioroebe/toplevel_methods/atomic_composition.rb +0 -198
  430. data/lib/bioroebe/toplevel_methods/base_composition.rb +0 -121
  431. data/lib/bioroebe/toplevel_methods/blast.rb +0 -153
  432. data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +0 -57
  433. data/lib/bioroebe/toplevel_methods/cat.rb +0 -71
  434. data/lib/bioroebe/toplevel_methods/chunked_display.rb +0 -92
  435. data/lib/bioroebe/toplevel_methods/cliner.rb +0 -81
  436. data/lib/bioroebe/toplevel_methods/complement.rb +0 -58
  437. data/lib/bioroebe/toplevel_methods/convert_global_env.rb +0 -39
  438. data/lib/bioroebe/toplevel_methods/databases.rb +0 -73
  439. data/lib/bioroebe/toplevel_methods/delimiter.rb +0 -19
  440. data/lib/bioroebe/toplevel_methods/digest.rb +0 -81
  441. data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +0 -146
  442. data/lib/bioroebe/toplevel_methods/e.rb +0 -20
  443. data/lib/bioroebe/toplevel_methods/editor.rb +0 -21
  444. data/lib/bioroebe/toplevel_methods/esystem.rb +0 -22
  445. data/lib/bioroebe/toplevel_methods/exponential_growth.rb +0 -74
  446. data/lib/bioroebe/toplevel_methods/extract.rb +0 -56
  447. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +0 -269
  448. data/lib/bioroebe/toplevel_methods/frequencies.rb +0 -99
  449. data/lib/bioroebe/toplevel_methods/hamming_distance.rb +0 -60
  450. data/lib/bioroebe/toplevel_methods/infer.rb +0 -66
  451. data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +0 -101
  452. data/lib/bioroebe/toplevel_methods/levensthein.rb +0 -63
  453. data/lib/bioroebe/toplevel_methods/log_directory.rb +0 -109
  454. data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +0 -55
  455. data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +0 -88
  456. data/lib/bioroebe/toplevel_methods/matches.rb +0 -259
  457. data/lib/bioroebe/toplevel_methods/misc.rb +0 -596
  458. data/lib/bioroebe/toplevel_methods/nucleotides.rb +0 -787
  459. data/lib/bioroebe/toplevel_methods/number_of_clones.rb +0 -63
  460. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +0 -79
  461. data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +0 -236
  462. data/lib/bioroebe/toplevel_methods/opn.rb +0 -34
  463. data/lib/bioroebe/toplevel_methods/palindromes.rb +0 -155
  464. data/lib/bioroebe/toplevel_methods/parse.rb +0 -59
  465. data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +0 -68
  466. data/lib/bioroebe/toplevel_methods/rds.rb +0 -24
  467. data/lib/bioroebe/toplevel_methods/remove.rb +0 -86
  468. data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +0 -35
  469. data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +0 -68
  470. data/lib/bioroebe/toplevel_methods/rna_splicing.rb +0 -73
  471. data/lib/bioroebe/toplevel_methods/rnalfold.rb +0 -69
  472. data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +0 -116
  473. data/lib/bioroebe/toplevel_methods/shuffleseq.rb +0 -37
  474. data/lib/bioroebe/toplevel_methods/statistics.rb +0 -53
  475. data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +0 -62
  476. data/lib/bioroebe/toplevel_methods/three_delimiter.rb +0 -34
  477. data/lib/bioroebe/toplevel_methods/time_and_date.rb +0 -53
  478. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +0 -31
  479. data/lib/bioroebe/toplevel_methods/truncate.rb +0 -48
  480. data/lib/bioroebe/toplevel_methods/url.rb +0 -36
  481. data/lib/bioroebe/toplevel_methods/verbose.rb +0 -59
  482. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -31
  483. data/lib/bioroebe/utility_scripts/showorf/help.rb +0 -33
  484. data/lib/bioroebe/utility_scripts/showorf/initialize.rb +0 -52
  485. data/lib/bioroebe/utility_scripts/showorf/menu.rb +0 -68
  486. data/lib/bioroebe/utility_scripts/showorf/reset.rb +0 -36
  487. data/lib/bioroebe/utility_scripts/showorf/run.rb +0 -152
  488. data/lib/bioroebe/utility_scripts/showorf/show.rb +0 -97
  489. /data/doc/{german_names_for_the_aminoacids.md → german_names_for_the_aminoacids/german_names_for_the_aminoacids.md} +0 -0
  490. /data/doc/{pdb_ATOM_entry.md → pdb_ATOM_entry/pdb_ATOM_entry.md} +0 -0
  491. /data/doc/{resources.md → resources/resources.md} +0 -0
  492. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/customized_dialog.rb +0 -0
  493. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/anti_sense_strand/anti_sense_strand.config +0 -0
  494. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +0 -0
  495. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +0 -0
  496. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/hamming_distance/hamming_distance.config +0 -0
  497. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/levensthein_distance/levensthein_distance.config +0 -0
  498. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/protein_to_DNA/protein_to_DNA.config +0 -0
  499. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.config +0 -0
  500. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.config +0 -0
  501. /data/lib/bioroebe/yaml/{base_composition_of_dna.yml → base_composition_of_dna/base_composition_of_dna.yml} +0 -0
  502. /data/lib/bioroebe/yaml/{nuclear_localization_sequences.yml → nuclear_localization_sequences/nuclear_localization_sequences.yml} +0 -0
  503. /data/lib/bioroebe/yaml/{talens.yml → talens/talens.yml} +0 -0
data/doc/todo/bioroebe_todo.md CHANGED
@@ -1,38 +1,77 @@
1
1
  --------------------------------------------------------------------------------
2
+ https://pepdraw.com/
3
+ ^^^ integrate this
4
+ --------------------------------------------------------------------------------
5
+ W D E N N M
6
+ NH2-Trp-Asp-Glu-Asn-Asn-Met-COOH
7
+
8
+ Nach dem genetischen Code wird dieses Hexa-
9
+ peptid von folgender DNA-Sequenz codiert:
10
+
11
+ to_aa TGG-GAT-GAA-AAT-AAT-ATG
12
+ to_aa TGG-GAC-GAG-AAC-AAC-ATG
13
+
14
+ to_codon W D E N N M
15
+
16
+ ^^^^ bioroebe: show_all_codons from commandline
17
+ AND document this also in the doc
18
+ es also 16 Oligonucleotide,
19
+ welche die Sequenz Trp-Asp-Glu-Asn-Asn-Met
20
+ codieren.
21
+
22
+ deduce WDENNM
23
+ ^^^^ show all of them!!!!
24
+ ^aka show ALL possible codons
25
+ --------------------------------------------------------------------------------
26
+ add support for
27
+
28
+ class Cell
29
+ class Immunoglobulin
30
+ hmmm
31
+ then add
32
+
33
+ class B_cell
34
+ class T_cell
35
+ class Macrophage
36
+ ^^^^ for testing purposes mostly
37
+ And then perhaps a few more cells. And we need to
38
+ add features to these.
39
+
40
+ --------------------------------------------------------------------------------
41
+ (1) → add support for:
42
+ codon_of? this_aminoacid
43
+ class CodonOfThisAminoacid
44
+ ^^^^ ^^^^^^
45
+ --------------------------------------------------------------------------------
2
46
  (2) → Integrate http://nc2.neb.com/NEBcutter2/cutshow.php?name=ffe1d68e-
3
47
  in particular the visual part.
4
48
  --------------------------------------------------------------------------------
5
- (3) → add support for:
6
- codon_of? this_aminoacid
7
- class CodonOfThisAminoacid
8
- ^^^^
9
- --------------------------------------------------------------------------------
10
- (4) → Bioroebe::RestrictionEnzymes::Statistics.show
49
+ (3) → Bioroebe::RestrictionEnzymes::Statistics.show
11
50
  ^^^ improve these
12
51
  and then add it to the documentation.
13
52
  --------------------------------------------------------------------------------
14
- (5) → use glimmer + nebula for widgets
53
+ (4) → use glimmer + nebula for widgets
15
54
  ^^^
16
55
  improve the nucleotide sequence analyser
17
56
  --------------------------------------------------------------------------------
18
- (6) → add to sinatra: a standalone server to query BAM files (and
57
+ (5) → add to sinatra: a standalone server to query BAM files (and
19
58
  the corresponding reference). The server will return the
20
59
  content of a BAM file in the selected folder when the
21
60
  server is started up. The server used is sintra.
22
61
  --------------------------------------------------------------------------------
23
- (7) → add the possibility to show what the effect of enzymes
62
+ (6) → add the possibility to show what the effect of enzymes
24
63
  are
25
64
  AND inhibitors of enzymes. perhaps bioroebe can be
26
65
  used in system biology one day
27
66
  --------------------------------------------------------------------------------
28
- (8) → Bioroebe::Sequence.new('AGCTTAGCGTACAGCTACGACGTAGTCTGACGA').cut_with? :AluI
67
+ (7) → Bioroebe::Sequence.new('AGCTTAGCGTACAGCTACGACGTAGTCTGACGA').cut_with? :AluI
29
68
  ^^^ support this API and document it too
30
69
  --------------------------------------------------------------------------------
31
- (9) → integrate electrno microscopy slowly and also add documentation
70
+ (8) → integrate electrno microscopy slowly and also add documentation
32
71
  about this AS YOU GO!!!!!
33
72
  ^^^ yup add more of it
34
73
  --------------------------------------------------------------------------------
35
- (10) → Add save session support
74
+ (9) → Add save session support
36
75
  to reload our last activity completely ...
37
76
  hmmm..
38
77
  This has to be well designed...
@@ -47,7 +86,7 @@
47
86
  upon startup of the bioroebe shell.
48
87
  This is in preparation for save-session support.
49
88
  --------------------------------------------------------------------------------
50
- (11) → Lys-Asp-Glu-Leu
89
+ (10) → Lys-Asp-Glu-Leu
51
90
  if i.include?('-') and Bioroebe.is_in_the_three_letter_code?(i)
52
91
  end
53
92
  - Lys-Asp-Glu-Leu-COO-
@@ -59,10 +98,10 @@
59
98
  ^^ yep this is also called KDEL
60
99
  https://en.wikipedia.org/wiki/KDEL_(amino_acid_sequence)
61
100
  --------------------------------------------------------------------------------
62
- (12) → Add "orthologs". this shall show us the top 25 orthologs or
101
+ (11) → Add "orthologs". this shall show us the top 25 orthologs or
63
102
  something. In the bioshell? Hmm. Not sure yet.
64
103
  --------------------------------------------------------------------------------
65
- (13) → clone the functionality of this:
104
+ (12) → clone the functionality of this:
66
105
  http://www.kazusa.or.jp/codon/cgi-bin/countcodon.cgi
67
106
  http://www.kazusa.or.jp/codon/countcodon.html
68
107
  In other words, create a class that can generate such an output.
@@ -72,15 +111,15 @@
72
111
  widget first. And sinatra output too.
73
112
  AND document it as well
74
113
  --------------------------------------------------------------------------------
75
- (14) → SARS genom analyisere in bioroebe
114
+ (13) → SARS genom analyisere in bioroebe
76
115
  eventuell auch graphisch
77
116
  Gibt es neue GUIs die wir kombinieren könnten? Hmmm.
78
117
  --------------------------------------------------------------------------------
79
- (15) → In bioroebe, generate that .ps thingy graphical thing from the
118
+ (14) → In bioroebe, generate that .ps thingy graphical thing from the
80
119
  vienna RNA tutorial. Hmmm.
81
120
  https://www.tbi.univie.ac.at/RNA/tutorial/
82
121
  --------------------------------------------------------------------------------
83
- (16) → get insulin squence frmo NCBI
122
+ (15) → get insulin squence frmo NCBI
84
123
  human
85
124
  then apply trypsin onto it
86
125
  and try it like this:
@@ -92,12 +131,12 @@
92
131
  ^^^ to show it
93
132
  Hmm. Perhaps also auto-download or something.
94
133
  --------------------------------------------------------------------------------
95
- (17) → in bioroebe: UAG?
134
+ (16) → in bioroebe: UAG?
96
135
  ^^^ show all stop codons with that in the bioshell
97
136
  all UAG sequences... hmm. and TAG?
98
137
  Finish that.
99
138
  --------------------------------------------------------------------------------
100
- (18) → The position of a symbol in a string is the total number of
139
+ (17) → The position of a symbol in a string is the total number of
101
140
  symbols found to its left, including itself (e.g., the positions
102
141
  of all occurrences of 'U' in "AUGCUUCAGAAAGGUCUUACG" are 2, 5,
103
142
  6, 15, 17, and 18). The symbol at position i
@@ -105,10 +144,10 @@
105
144
  ^^^ add a solution there, a toplevel API
106
145
  !!!!!
107
146
  --------------------------------------------------------------------------------
108
- (19) → http://bioruby.org/rdoc/Bio/Blast.html
147
+ (18) → http://bioruby.org/rdoc/Bio/Blast.html
109
148
  ^^^ add support for BLAST
110
149
  --------------------------------------------------------------------------------
111
- (20) → add: parse_pdb()
150
+ (19) → add: parse_pdb()
112
151
  With this we shall just show some info, about a given
113
152
  .pdb file at hand.
114
153
  Also make it commandline based too + bioshell variant
@@ -116,55 +155,55 @@
116
155
  Don't forget to document it!!!!!
117
156
  ^^^ and google a bit how others do that
118
157
  --------------------------------------------------------------------------------
119
- (21) → pdb 1a6m
158
+ (20) → pdb 1a6m
120
159
  ^^^ download this when that is used in the bioshell; we also have
121
160
  to use the download directory for this, so make sure that
122
161
  we do.
123
162
  ^^^ And then, also document this clearly.
124
163
  --------------------------------------------------------------------------------
125
- (22) → show_string
164
+ (21) → show_string
126
165
  ^^^ slowly port this ... find out differences
127
166
  then unify into one method. right now we used
128
167
  two or something.
129
168
  --------------------------------------------------------------------------------
130
- (23) → Try to see if we can integrate this into our GUI:
169
+ (22) → Try to see if we can integrate this into our GUI:
131
170
  https://cdn.snapgene.com/assets/7.6.11/assets/images/snapgene/homepage/homepage-hero.png
132
171
  --------------------------------------------------------------------------------
133
- (24) → Scan for leucine zipper!
172
+ (23) → Scan for leucine zipper!
134
173
  This is ~25% implemented. We need to double-check what
135
174
  exactly is a leucine zipper.
136
175
  --------------------------------------------------------------------------------
137
- (25) → Extend the sinatra-interface for the Rosalind task,
176
+ (24) → Extend the sinatra-interface for the Rosalind task,
138
177
  perhaps add a sub-link to show which parts are solved
139
178
  as-is. Hmm. I am not continuing on this though.
140
179
  ^^^^
141
180
  well - make rosalind anew again or something.
142
181
  --------------------------------------------------------------------------------
143
- (26) → Add a blast interface; both via the web-interface, GUI,
182
+ (25) → Add a blast interface; both via the web-interface, GUI,
144
183
  and also from the commandline.
145
184
  --------------------------------------------------------------------------------
146
- (27) → Write a tutorial about primer design.
185
+ (26) → Write a tutorial about primer design.
147
186
  also make sure that the GUI has support for this.
148
187
  --------------------------------------------------------------------------------
149
- (28) → In the documentation examples, show some exampls for how to work
188
+ (27) → In the documentation examples, show some exampls for how to work
150
189
  with different organisms.
151
190
  --------------------------------------------------------------------------------
152
- (29) → In the bioshell, if "stop?" is issued, then the colouring isn't
191
+ (28) → In the bioshell, if "stop?" is issued, then the colouring isn't
153
192
  correct. It currently does not show any result. This has to
154
193
  be fixed.
155
194
  --------------------------------------------------------------------------------
156
- (30) → https://www.rubydoc.info/gems/biomart
195
+ (29) → https://www.rubydoc.info/gems/biomart
157
196
  ^^^ integrate biomart
158
197
  p biomart.list_datasets
159
198
  p biomart.datasets?
160
199
  --------------------------------------------------------------------------------
161
- (31) → Add Trypsin und Trypsinogen sequences, both as FASTA
200
+ (30) → Add Trypsin und Trypsinogen sequences, both as FASTA
162
201
  but also as shortcut via the commandline such as:
163
202
  show_orf :trypsine
164
203
  show_orf :trypsin
165
204
  Or something like this; and document it as well.
166
205
  --------------------------------------------------------------------------------
167
- (32) → 1..60
206
+ (31) → 1..60
168
207
  setdna 57
169
208
  append stop
170
209
  1..60
@@ -174,12 +213,12 @@
174
213
  ^^^ hier beim colourize, wenn das letzte codon ein STOP codon ist
175
214
  dann colourizen wir das auch.
176
215
  --------------------------------------------------------------------------------
177
- (33) → MG1655
216
+ (32) → MG1655
178
217
  ^^^ input this to download the sequence. Also show it to the user.
179
218
  --------------------------------------------------------------------------------
180
- (34) → extend virus-information into the bioroebe project.
219
+ (33) → extend virus-information into the bioroebe project.
181
220
  --------------------------------------------------------------------------------
182
- (35) → Add a way to analyse the chemical structure of all
221
+ (34) → Add a way to analyse the chemical structure of all
183
222
  aminoacids. We wish to show the chemical formula.
184
223
  E. g. if we input:
185
224
  "phenylalanin"
@@ -189,22 +228,22 @@
189
228
  I don't understand why it removes H and 0 so perhaps
190
229
  dont remove that part. But still show the -R.
191
230
  --------------------------------------------------------------------------------
192
- (36) → FIX THE COLOURIZATION BUG; THIS ONE TRIGGERED THE WHOLE
231
+ (35) → FIX THE COLOURIZATION BUG; THIS ONE TRIGGERED THE WHOLE
193
232
  REWRITE AFTER ALL!
194
233
  --------------------------------------------------------------------------------
195
- (37) → FIX TAXONOMY related-problems AS WELL
234
+ (36) → FIX TAXONOMY related-problems AS WELL
196
235
  ^^^^^^ AND DOCUMENT THIS related-problems.
197
236
  --------------------------------------------------------------------------------
198
- (38) → Do note that z will then be a String, not a sequence object anymore.
237
+ (37) → Do note that z will then be a String, not a sequence object anymore.
199
238
  (This may be subject to change in the future, but for now, aka
200
239
  **February 2020**, it is that way.)
201
240
  ^^^^
202
241
  --------------------------------------------------------------------------------
203
- (39) → ^^^ colours are appended. That should not be the case!
242
+ (38) → ^^^ colours are appended. That should not be the case!
204
243
  ADD SOMETHING NEW ... some todo entries
205
244
  and some python tool
206
245
  --------------------------------------------------------------------------------
207
- (40) → rewrite the whole project anew
246
+ (39) → rewrite the whole project anew
208
247
  - improve the documentation
209
248
  - focus on class Protein first and add
210
249
  all_dna_combinations or somethingl ike
@@ -212,7 +251,7 @@
212
251
  .backtrans
213
252
  .reverse_translate
214
253
  --------------------------------------------------------------------------------
215
- (41) →
254
+ (40) →
216
255
  Reduced alphabets for proteins | [not implemented yet]
217
256
  ^^^ check this as well
218
257
  require 'bioroebe/base/commandline_application/aminoacids.rb'
@@ -235,9 +274,9 @@
235
274
  efetch "https://www.ncbi.nlm.nih.gov/gene/744779"
236
275
  ^^^ test this. again
237
276
  --------------------------------------------------------------------------------
238
- (42) → fix tk-levensthein
277
+ (41) → fix tk-levensthein
239
278
  --------------------------------------------------------------------------------
240
- (43) → rewrite the whole project anew
279
+ (42) → rewrite the whole project anew
241
280
  - improve the documentation
242
281
  - rework the WHOLE tutorial as well
243
282
  - focus on class Protein first and add
@@ -246,12 +285,12 @@
246
285
  .backtrans
247
286
  .reverse_translate
248
287
  --------------------------------------------------------------------------------
249
- (44) → analyze /Depot/Temp/Bioroebe/1CEZ.pdb
288
+ (43) → analyze /Depot/Temp/Bioroebe/1CEZ.pdb
250
289
  ^^^
251
290
  support this. Already works half-way, we started writing a pdb parser.
252
291
  this should work in general, for .fasta files as well.
253
292
  --------------------------------------------------------------------------------
254
- (45) → SINATRA STUFF:
293
+ (44) → SINATRA STUFF:
255
294
  FIX AND EXTEND SINATRA IN BIOROEBE.
256
295
  extend it too.
257
296
  http://localhost:4567/random_aminoacids
@@ -261,7 +300,7 @@
261
300
  where the nucleotide sequence has numbers
262
301
  ^^^
263
302
  --------------------------------------------------------------------------------
264
- (46) → pick any virus and begin to amass tons of data; and then when done
303
+ (45) → pick any virus and begin to amass tons of data; and then when done
265
304
  also connect this into a GUI for use therein.
266
305
  See:
267
306
  https://raw.githubusercontent.com/labsquare/fastQt/master/screenshot.gif
@@ -272,15 +311,15 @@
272
311
  research about circovirus too
273
312
  https://www.ncbi.nlm.nih.gov/nuccore/NC_038391.1
274
313
  --------------------------------------------------------------------------------
275
- (47) → Fix:
314
+ (46) → Fix:
276
315
  require 'bioroebe/toplevel_methods/open_reading_frames.rb'
277
316
  Something is wrong; it returns regions that contain
278
317
  a stop codon, which can not be true.
279
318
  --------------------------------------------------------------------------------
280
- (48) → Fix: extend glycovirology parts
319
+ (47) → Fix: extend glycovirology parts
281
320
  seek stuff in viral genomes
282
321
  --------------------------------------------------------------------------------
283
- (49) →
322
+ (48) →
284
323
  seq = Bio::Sequence::NA.new("atgcatgcaaaaaaa")
285
324
  puts seq
286
325
  puts seq.complement
@@ -302,7 +341,7 @@
302
341
  puts seq
303
342
  puts seq.complement
304
343
  --------------------------------------------------------------------------------
305
- (50) → In BioRoebe:
344
+ (49) → In BioRoebe:
306
345
  Add a table showing how compatible bioroebe is compared to the other
307
346
  bio-projects, staring with biophp.
308
347
  Also show the status how much is complete in each,
@@ -310,7 +349,7 @@
310
349
  And add a table which functionality is implemented
311
350
  in Java already.
312
351
  --------------------------------------------------------------------------------
313
- (51) →
352
+ (50) →
314
353
  ********************************************************************************
315
354
  Was passiert wenn wir das Lambda-Genom mit EcoRI behandeln?
316
355
  ********************************************************************************
@@ -329,11 +368,11 @@
329
368
  ^^^ this now works kind of ... but it must be better
330
369
  documented and we must test this with more data.
331
370
  --------------------------------------------------------------------------------
332
- (52) → https://international.neb.com/products/r0196-ncii#Product%20Information
371
+ (51) → https://international.neb.com/products/r0196-ncii#Product%20Information
333
372
  ^^^ autogenerate such an image, aka restriction cutting enzyme
334
373
  to indicate the target sequence.
335
374
  --------------------------------------------------------------------------------
336
- (53) → how to do codon optimiation in e.coli? bioroebe must support this!
375
+ (52) → how to do codon optimiation in e.coli? bioroebe must support this!
337
376
  we must first get a display which codon is very commonly used in
338
377
  E. coli, from some remote site ... japanese site I think.
339
378
  then, we analyse all possibilities.
@@ -341,19 +380,19 @@
341
380
  them on the commandline
342
381
  class: OptimizeCodons.new(of_this_sequence)
343
382
  --------------------------------------------------------------------------------
344
- (54) → Molekulare Grösse von "Ubiquitin"? "8.5 kd".
383
+ (53) → Molekulare Grösse von "Ubiquitin"? "8.5 kd".
345
384
  ^^^ das sollte automatisch ausgerechnet werden
346
385
  --------------------------------------------------------------------------------
347
- (55) → taxonomy !!!!!!!!!!!!!!!!!!
386
+ (54) → taxonomy !!!!!!!!!!!!!!!!!!
348
387
  --------------------------------------------------------------------------------
349
- (56) → Given a list of gene names that I would like to get chromosome/position
388
+ (55) → Given a list of gene names that I would like to get chromosome/position
350
389
  information for (in mm10). Is there some service online where I can
351
390
  paste this list? ^^^ enable this
352
391
  --------------------------------------------------------------------------------
353
- (57) → Make bioroebe very useful from the www, no matter if via sinatra
392
+ (56) → Make bioroebe very useful from the www, no matter if via sinatra
354
393
  or rails. It should be a tool-set project on the www as well.
355
394
  --------------------------------------------------------------------------------
356
- (58) → Suppose you have a GenBank file which you want to turn into a
395
+ (57) → Suppose you have a GenBank file which you want to turn into a
357
396
  Fasta file. For example, lets consider the file cor6_6.gb
358
397
  which is included in the Biopython unit tests under the
359
398
  GenBank directory.
@@ -364,26 +403,26 @@
364
403
  the GUI works somewhat but needs to be polished up.
365
404
  THEN THIS CAN BE REMOVED!!!!!!!
366
405
  --------------------------------------------------------------------------------
367
- (59) → Wir brauchen eine table wo wir die starken promotoren verschiedener
406
+ (58) → Wir brauchen eine table wo wir die starken promotoren verschiedener
368
407
  Organismen zusammenstellen und vergleichen können.
369
408
  strong_promoters.yml
370
409
  --------------------------------------------------------------------------------
371
- (60) → add:
410
+ (59) → add:
372
411
  start position of exons
373
412
  and show the sequence based on that file
374
413
  Normally there's a "gene" entry for each gene, so:
375
414
  awk 'BEGIN{FS="\t"; OFS="\t"}{if($3 == "gene") print $1, $4, $5}' foo.gtf
376
415
  --------------------------------------------------------------------------------
377
- (61) → also add 30-33 to aminoacids hmmm difficult.
416
+ (60) → also add 30-33 to aminoacids hmmm difficult.
378
417
  --------------------------------------------------------------------------------
379
- (62) → http://bioinformatics.oxfordjournals.org/content/18/8/1135
418
+ (61) → http://bioinformatics.oxfordjournals.org/content/18/8/1135
380
419
  "TFBS: Computational framework for transcription factor
381
420
  binding site analysis"
382
421
  study the above and see if it can be included
383
422
  into bioroebe
384
423
  http://tfbs.genereg.net/
385
424
  --------------------------------------------------------------------------------
386
- (63) → They include trypsin, chymotrypsin, thrombin, plasmin, papain and factor Xa.
425
+ (62) → They include trypsin, chymotrypsin, thrombin, plasmin, papain and factor Xa.
387
426
  ^^^ provide means to identify where they cut,
388
427
  and show this then by simualting a digest.
389
428
  return an array with the starting aminoacids.
@@ -391,7 +430,7 @@
391
430
  this is done via digestion/digestions
392
431
  but it's not quite perfect yet.
393
432
  --------------------------------------------------------------------------------
394
- (64) → a) add a commandline way to generate a random protein
433
+ (63) → a) add a commandline way to generate a random protein
395
434
  with a specified length and then display it on the
396
435
  commandline [DONE] !!!
397
436
  bioroebe --random-aminoacids=33
@@ -411,26 +450,26 @@
411
450
  Enable this BOTH from the commandline AND from the
412
451
  interactive variant and from sinatra! Hmmmm.
413
452
  --------------------------------------------------------------------------------
414
- (65) → add an option to design a
453
+ (64) → add an option to design a
415
454
  degenerate primer
416
455
  --------------------------------------------------------------------------------
417
- (66) → Add upcase to sequences and ensure that it works; also document it
456
+ (65) → Add upcase to sequences and ensure that it works; also document it
418
457
  internally and in the .pdf tutorial
419
458
  what does that mean? upcase as method? hmmm.
420
459
  --------------------------------------------------------------------------------
421
- (67) → http://www.biomart.org/other/user-docs.pdf
460
+ (66) → http://www.biomart.org/other/user-docs.pdf
422
461
  ^^^ work through this
423
462
  ^^^ integrate the old .cgi part and improve as you go
424
463
  --------------------------------------------------------------------------------
425
- (68) → Access geninfo numbers easily.
464
+ (67) → Access geninfo numbers easily.
426
465
  Die suchen und runterladen.
427
466
  --------------------------------------------------------------------------------
428
- (69) → Add all of bioruby into bioroebe:
467
+ (68) → Add all of bioruby into bioroebe:
429
468
  continous project
430
469
  https://github.com/biopython/biopython
431
470
  https://github.com/bioruby/bioruby/tree/master/lib/bio
432
471
  --------------------------------------------------------------------------------
433
- (70) → https://github.com/bioruby/bioruby/issues/134
472
+ (69) → https://github.com/bioruby/bioruby/issues/134
434
473
  ^^^ check this, for restriction enzymes
435
474
  http://rebase.neb.com/rebase/enz/MboII.html
436
475
  Bio::RestrictionEnzyme.cut(seq, 'MboII').primary rescue [seq]
@@ -439,9 +478,9 @@
439
478
  > Bio::RestrictionEnzyme.cut(seq, 'MboII').primary rescue [seq]
440
479
  => ["atcatcaatcctaatcttct"]
441
480
  --------------------------------------------------------------------------------
442
- (71) → Document how an ORF is defined for the bioroebe project.
481
+ (70) → Document how an ORF is defined for the bioroebe project.
443
482
  --------------------------------------------------------------------------------
444
- (72) → Continue with biojava in bioroebe.
483
+ (71) → Continue with biojava in bioroebe.
445
484
  → We need to make some table that tells us what is implemented
446
485
  in java.
447
486
  → Make it possible to randomly generate aminoacids, and then,
@@ -451,7 +490,7 @@
451
490
  We can generate degenerate primers now:
452
491
  dprimer M-T-T-Y-Y-T-A-A-A-STOP
453
492
  --------------------------------------------------------------------------------
454
- (73) → The codon tables:
493
+ (72) → The codon tables:
455
494
  → In January we added a codon-table GUI to ruby-gtk3.
456
495
  also enable an inverse table.
457
496
  Ala/A GCT, GCC, GCA, GCG GCN Leu/L TTA, TTG, CTT, CTC, CTA, CTG YTR, CTN
@@ -474,26 +513,26 @@
474
513
  that we can now display all the different codon tables.
475
514
  This now sorta works semi-ok.
476
515
  --------------------------------------------------------------------------------
477
- (74) → In the bioroebe-shell, enable input such as:
516
+ (73) → In the bioroebe-shell, enable input such as:
478
517
  NC_000011.10
479
518
  This shall quickly download this sequence into the
480
519
  local file, and also rename it properly.
481
520
  --------------------------------------------------------------------------------
482
- (75) → clone all of bioruby
521
+ (74) → clone all of bioruby
483
522
  --------------------------------------------------------------------------------
484
- (76) → bioinf bücher udrhclesen und zeug inkludiere !!!
523
+ (75) → bioinf bücher udrhclesen und zeug inkludiere !!!
485
524
  ^^^^^ mehr bilderchen hinzufügen ... auchv on den GUIs eventuell.
486
525
  Und auch biopython durcharbeiten und alles wichtige nach
487
526
  bioroebe übertragen.
488
527
  --------------------------------------------------------------------------------
489
- (77) → Add: DetectMotif
528
+ (76) → Add: DetectMotif
490
529
  This class shall be used for detecting subsequences.
491
530
  --------------------------------------------------------------------------------
492
- (78) → Neue funktionälit rein
531
+ (77) → Neue funktionälit rein
493
532
  --------------------------------------------------------------------------------
494
- (79) → mehr doku!!!
533
+ (78) → mehr doku!!!
495
534
  --------------------------------------------------------------------------------
496
- (80) → Rewrite bioroebe completely - add some tests, too or so, to
535
+ (79) → Rewrite bioroebe completely - add some tests, too or so, to
497
536
  test this. ^^^
498
537
  That way we learn how to write tests.
499
538
  AND ... we will actually start with the taxonomy project
@@ -533,7 +572,7 @@
533
572
  also add a footer to show which entries are available or so
534
573
  → in bioroebe, mach das die postgresql datenbank wieder funktioniert ...
535
574
  --------------------------------------------------------------------------------
536
- (81) → ^^^ improve this whole project a lot
575
+ (80) → ^^^ improve this whole project a lot
537
576
  before uploading then send email
538
577
  → add:
539
578
  set_dna :insulin
@@ -546,28 +585,28 @@
546
585
  → becomes: http://www.ncbi.nlm.nih.gov/gene/3630
547
586
  wtf ... better to learn how NCBI uworks
548
587
  --------------------------------------------------------------------------------
549
- (82) → Add a seuqence table into bioroebe for GFP, YFP etc
588
+ (81) → Add a seuqence table into bioroebe for GFP, YFP etc
550
589
  and mae this show in both the interactio bioshell but
551
590
  also the main README.md
552
591
  --------------------------------------------------------------------------------
553
- (83) → http://www.biophp.org/stats/describe_data/demo.php?show=formula
592
+ (82) → http://www.biophp.org/stats/describe_data/demo.php?show=formula
554
593
  ^^^ should also add documentation like this, also via www interface
555
594
  --------------------------------------------------------------------------------
556
- (84) → Add a "cutter-range example" in restriction enzymes +
595
+ (83) → Add a "cutter-range example" in restriction enzymes +
557
596
  table + examples + tutorial
558
597
  one example each in this overview.
559
598
  Also, add in the documentation where this
560
599
  can be found.
561
600
  --------------------------------------------------------------------------------
562
- (85) → Add some codon-usage analyzer. What shall it show? It
601
+ (84) → Add some codon-usage analyzer. What shall it show? It
563
602
  should show how many codons are used, frequencies etc...
564
603
  by an organism, and compare that to other data.
565
604
  --------------------------------------------------------------------------------
566
- (86) → Implement a GPCR interface.
605
+ (85) → Implement a GPCR interface.
567
606
  This is for "G-protein coupled receptors."
568
607
  Denote which variants exist and so forth. Document it as well.
569
608
  --------------------------------------------------------------------------------
570
- (87) → alu?
609
+ (86) → alu?
571
610
  Will read from the file `/Programs/Ruby/2.3.0/lib/ruby/site_ruby/2.3.0/bioroebe/yaml/alu_elements.yml`.
572
611
  Bioroebe::ParseFasta: This sequence is assumed to be a protein.
573
612
  This sequence has 1317 aminoacids.
@@ -583,7 +622,7 @@
583
622
  And perhaps add a small protein as an example how to
584
623
  work with .pdb files instead.
585
624
  --------------------------------------------------------------------------------
586
- (88) → Extend bioroebe to allow download
625
+ (87) → Extend bioroebe to allow download
587
626
  PDB files
588
627
  id 3030
589
628
  and then display nice thingies to the user.
@@ -592,35 +631,35 @@
592
631
  in 3EML 2VTP 2VEZ
593
632
  do
594
633
  --------------------------------------------------------------------------------
595
- (89) → Fully integrate electron microscopy then remove the old entry.
634
+ (88) → Fully integrate electron microscopy then remove the old entry.
596
635
  Test it though.
597
636
  Hmm... but ... we will first polish the main bioroebe
598
637
  gem AND the taxonomy gem and THEN AFTERWARDS
599
638
  integate elctron microsopcy.
600
639
  --------------------------------------------------------------------------------
601
- (90) → ORF Finder:
640
+ (89) → ORF Finder:
602
641
  We must add an ORF finder for the bioroebe project,
603
642
  similar to the NCBI ORF Finder.
604
643
  This works partially... start_stop works but we do not
605
644
  yet find all subsequences.
606
645
  --------------------------------------------------------------------------------
607
- (91) → must change determine whether we have protein or nucleotide or
646
+ (90) → must change determine whether we have protein or nucleotide or
608
647
  so via a topelvel method!
609
648
  --------------------------------------------------------------------------------
610
- (92) → there is a talens module.
649
+ (91) → there is a talens module.
611
650
  we have to improve on it for a while
612
651
  better docu
613
652
  more testing
614
653
  then we can get rid of this entry here
615
654
  --------------------------------------------------------------------------------
616
- (93) → 33.44
655
+ (92) → 33.44
617
656
  Next showing the nucleotides 33 to 44 (including 33 and 44).
618
657
  The length of the fragment will be 12 nucleotides.
619
658
  5' - 2;70;130;180 - 3'
620
659
  ^^^ there is some problem; we somehow embed the colour codes,
621
660
  which should not happen.
622
661
  --------------------------------------------------------------------------------
623
- (94) → set_aa DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STASSWSYIV ETSNSDNGTC YPGDFINYEE LREQLSSVSS FERFEIFPKT SSWPNHDNKG VTAACPHAGA KSFYKNLIWL VKKGNSYPKL NQSYINDKGK EVLVLWGIHH PSTTADQQSL YQNADAYVFV GTSRYSKKFK PEIATRPKVR DQEGRMNYYW TLVEPGDKIT FEATGNLVVP RYAFMERNAG SGIIISDTPV HDCNTTCQTP EGAINTSLPF QNIHPITIGK CPKYVKSTKL RLATGLRNVP SIQSRGLFGA IAGFIEGGWT GMVDGWYGYH HQNEQGSGYA ADLKSTQNAI DKITNKVNSV IKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRNQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREKIDGV KLESTRIYHH HHHH
662
+ (93) → set_aa DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STASSWSYIV ETSNSDNGTC YPGDFINYEE LREQLSSVSS FERFEIFPKT SSWPNHDNKG VTAACPHAGA KSFYKNLIWL VKKGNSYPKL NQSYINDKGK EVLVLWGIHH PSTTADQQSL YQNADAYVFV GTSRYSKKFK PEIATRPKVR DQEGRMNYYW TLVEPGDKIT FEATGNLVVP RYAFMERNAG SGIIISDTPV HDCNTTCQTP EGAINTSLPF QNIHPITIGK CPKYVKSTKL RLATGLRNVP SIQSRGLFGA IAGFIEGGWT GMVDGWYGYH HQNEQGSGYA ADLKSTQNAI DKITNKVNSV IKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRNQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREKIDGV KLESTRIYHH HHHH
624
663
  ^^^ enable copy/pasting,
625
664
  then reverse_sequence
626
665
  dna_sequence?
@@ -631,7 +670,7 @@
631
670
  This sequence has 50 aminoacids.
632
671
  ^^^ das stimmt net.
633
672
  --------------------------------------------------------------------------------
634
- (95) → add this functionality:
673
+ (94) → add this functionality:
635
674
  meting temper
636
675
  melting temper
637
676
  melting_temperature?
@@ -659,44 +698,44 @@
659
698
  using ruby. The latter may be useful and rather easy for
660
699
  scripted use.
661
700
  --------------------------------------------------------------------------------
662
- (96) → show insulin
701
+ (95) → show insulin
663
702
  ^^^ to show the insulin structure
664
703
  how to find it? no idea...
665
704
  but we should have these structures already made available somewhere.
666
705
  --------------------------------------------------------------------------------
667
- (97) → Todo: find family of enzymes, based on sequence structure
706
+ (96) → Todo: find family of enzymes, based on sequence structure
668
707
  alone.
669
708
  --------------------------------------------------------------------------------
670
- (98) → WORK THROUGH the PROTOCOL AT BOKU. THEN WORK THROUGH THE VARIOUST
709
+ (97) → WORK THROUGH the PROTOCOL AT BOKU. THEN WORK THROUGH THE VARIOUST
671
710
  TIDBIDS AT UNI WIEN STARTING WITH HEIKO.
672
711
  ^^^ da sind wir nun.
673
712
  wir sind an beginn von 1b ... hmmmm, also zerst mal das an der
674
713
  BOKU durchgehen. Dann das löschen.
675
714
  --------------------------------------------------------------------------------
676
- (99) → Begin tk-bindings for bioroebe, following the gtk stuff.
715
+ (98) → Begin tk-bindings for bioroebe, following the gtk stuff.
677
716
  --------------------------------------------------------------------------------
678
- (100) → frame_value = position_of_the_stop_codon - position_of_the_start_codon
717
+ (99) → frame_value = position_of_the_stop_codon - position_of_the_start_codon
679
718
  ^^^ continue on this ...
680
719
  --------------------------------------------------------------------------------
681
- (101) → improve both the gtk-apps parts, and the sinatra web-interface,
720
+ (100) → improve both the gtk-apps parts, and the sinatra web-interface,
682
721
  and other GUI-like elements. The idea is to make this software
683
722
  more useful for people around the world, which should help
684
723
  increase its adoption rate.
685
724
  --------------------------------------------------------------------------------
686
- (102) → Look to integrate this:
725
+ (101) → Look to integrate this:
687
726
  http://www.ncbi.nlm.nih.gov/nuccore/NM_007315.3?report=fasta&log$=seqview&format=text
688
727
  ^^^
689
728
  --------------------------------------------------------------------------------
690
- (103) → We need to make available the ... thingy magick
729
+ (102) → We need to make available the ... thingy magick
691
730
  emboss functionality. that may seem useful
692
731
  but also feel free to extend these parts for
693
732
  bioroebe as necessary.
694
733
  --------------------------------------------------------------------------------
695
- (104) → integrate electron_microscopy fully
734
+ (103) → integrate electron_microscopy fully
696
735
  This will take more time, so first we finish with the
697
736
  taxonomy module instead.
698
737
  --------------------------------------------------------------------------------
699
- (105) → Improve support for BLAST up until
738
+ (104) → Improve support for BLAST up until
700
739
  middle of 2015 so that I am better prepared
701
740
  for work-related stuff. In order for this
702
741
  to succed, we first have to understand
@@ -704,14 +743,14 @@
704
743
  So, work on BLAST tutorial at bioinf page:
705
744
  bl bioinf; rf bioinf
706
745
  --------------------------------------------------------------------------------
707
- (106) → integrate a "codon usage database", whatever this means.
746
+ (105) → integrate a "codon usage database", whatever this means.
708
747
  It is a cool database anyway. Then document this.
709
748
  First, create a codon-usage analyze on a per-FASTA
710
749
  site basis. Meaning we download a fasta sequence
711
750
  and calculate the codon usage from there.
712
751
  ^^^ and add some GUI to this. hmmm
713
752
  --------------------------------------------------------------------------------
714
- (107) → Input sequence:
753
+ (106) → Input sequence:
715
754
  MFLMVSPTAYHQNKDECFLP
716
755
  TAYHQNKDECMVSPTAYHQN
717
756
  KDECFLPTAYHQMVSPTAYH
@@ -724,42 +763,42 @@
724
763
  ^^^ we should also show this on the commandline AND the
725
764
  www ... hmmm.
726
765
  --------------------------------------------------------------------------------
727
- (108) → enable a graphical layer so that we can find out which
766
+ (107) → enable a graphical layer so that we can find out which
728
767
  transcription factor activates which gene(s). This
729
768
  should show e. g. a transcription factor highlighting
730
769
  a target genetic area.
731
770
  --------------------------------------------------------------------------------
732
- (109) → We should add more screenshots, make them available on imgur
771
+ (108) → We should add more screenshots, make them available on imgur
733
772
  as well, after storing them locally. Start with the more
734
773
  important functionality.
735
774
  --------------------------------------------------------------------------------
736
- (110) → clone serial cloner or whatever the name was, that GUI,
775
+ (109) → clone serial cloner or whatever the name was, that GUI,
737
776
  so that we can offer the same functionality.
738
777
  --------------------------------------------------------------------------------
739
- (111) →
778
+ (110) →
740
779
  # * searching for PubMed IDs given a query string:
741
780
  # * Bio::PubMed#esearch (recommended)
742
781
  # * Bio::PubMed#search (only retrieves top 20 hits; will be deprecated)
743
782
  ^^^ implement this
744
783
  --------------------------------------------------------------------------------
745
- (112) → Aufgabe 16 in bioroebe lösen könnnen
784
+ (111) → Aufgabe 16 in bioroebe lösen könnnen
746
785
  --------------------------------------------------------------------------------
747
- (113) → re1 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme1)
786
+ (112) → re1 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme1)
748
787
  ^^^ add this? hmmmm
749
788
  ^^^ from here.
750
789
  --------------------------------------------------------------------------------
751
- (114) → Colourize exon/intron boundaries.
790
+ (113) → Colourize exon/intron boundaries.
752
791
  --------------------------------------------------------------------------------
753
- (115) → In bioroebe: enhance phylogeny stuff and perhaps automatically
792
+ (114) → In bioroebe: enhance phylogeny stuff and perhaps automatically
754
793
  generate pictures here.
755
794
  --------------------------------------------------------------------------------
756
- (116) → In sinatra: add a backtranseq entry point, perhaps
795
+ (115) → In sinatra: add a backtranseq entry point, perhaps
757
796
  alias it as well.
758
797
  ^^ sync this to ruby-gtk3? hmm
759
798
  bioroebe --protein-to-dna
760
799
  ^^^ this shall start the GTK3 variant
761
800
  --------------------------------------------------------------------------------
762
- (117) → require 'rubygems/text'
801
+ (116) → require 'rubygems/text'
763
802
  include Gem::Text
764
803
  levenshtein_distance 'shevy', 'chevy' # => 1
765
804
  ^^^ add some class that outpus, on the commandline
@@ -768,13 +807,13 @@
768
807
  https://github.com/rubygems/rubygems/blob/master/lib/rubygems/text.rb
769
808
  ^^^ actually move that part into bioroebe itself...
770
809
  --------------------------------------------------------------------------------
771
- (118) → add _source to all APIs in sinatra there. Ensure that this works
810
+ (117) → add _source to all APIs in sinatra there. Ensure that this works
772
811
  too. The user should be able to view the source code.
773
812
  ^^^ it has been added for 2 methods so far in sinatra; we need
774
813
  to add it for the remaining ones too. Then we can remove
775
814
  this entry point.
776
815
  --------------------------------------------------------------------------------
777
- (119) → Check out expasy
816
+ (118) → Check out expasy
778
817
  peptidcutter
779
818
  also offer this functionality, through commandline, GUI
780
819
  and sinatra.
@@ -782,18 +821,18 @@
782
821
  We now have added trypsin but we should add more here; and
783
822
  still have to add support for sinatra here.
784
823
  --------------------------------------------------------------------------------
785
- (120) → melting temperature subsection
824
+ (119) → melting temperature subsection
786
825
  hmmm .... molecular weight calculation works now ... but
787
826
  ... is it correct for a ssDNA string? hmm...
788
827
  --------------------------------------------------------------------------------
789
- (121) → Degenerate Primers
828
+ (120) → Degenerate Primers
790
829
  You can try to determine the degenerate primers via the Shell
791
830
  component. Issue the following instructions:
792
831
  degenerate_primer
793
832
  ^^^ epxnad that subsection
794
833
  more explanations and examples
795
834
  --------------------------------------------------------------------------------
796
- (122) → Copy the functionality of plotorf:
835
+ (121) → Copy the functionality of plotorf:
797
836
  See:
798
837
  http://www.bioinformatics.nl/cgi-bin/emboss/plotorf
799
838
  Also extend emboss info on the main homepage.
@@ -803,44 +842,44 @@
803
842
  ^^^
804
843
  Bioroebe.return_all_ORFS
805
844
  --------------------------------------------------------------------------------
806
- (123) → Start nucleotide position is at: 142
845
+ (122) → Start nucleotide position is at: 142
807
846
  See the following example:
808
847
  BIO SHELL> highlight AAA
809
848
  5' - GTAACTGTTAAACTGTCAGGCAGGCGCTCAGGTGTACGTTTGATGCTCAGTAGTATTCCATTCTCGCGAGGGTCACGATACCCAAGATCTCCATGGCTTTCTGTTAGACGCAGCCGTGGACGACTAGAGCGTTTTTTTTTGGAAAGTATATGACCAGCACTCTACATCCTAACTAGAAGGTCTTCTAGGCGTACCAATATTAACGAATAGTGAGTGGTTACCCGTACCCGTCATGACGTCTATCATTAATT - 3'
810
849
  BIO SHELL>
811
850
  ^^^ this does not work; nothing is highlighted.
812
851
  --------------------------------------------------------------------------------
813
- (124) → Add a myristoylierung-signal
852
+ (123) → Add a myristoylierung-signal
814
853
  Met-Gly-Xaa-Xaa-YXaa-Ser/Thr-Lys-Lys
815
854
  1^^ but check first.
816
855
  --------------------------------------------------------------------------------
817
- (125) → integrate the bioroebe_tutorial.cgi into the .md file completely.
856
+ (124) → integrate the bioroebe_tutorial.cgi into the .md file completely.
818
857
  --------------------------------------------------------------------------------
819
- (126) → Integrate everything from the biopython tutorial, if it makes
858
+ (125) → Integrate everything from the biopython tutorial, if it makes
820
859
  sense.
821
860
  --------------------------------------------------------------------------------
822
- (127) → Improve the codon-optimizer in Bioroebe, including the
861
+ (126) → Improve the codon-optimizer in Bioroebe, including the
823
862
  documentation. We need to make this really useful.
824
863
  --------------------------------------------------------------------------------
825
- (128) →
864
+ (127) →
826
865
  5'- TACACGGCACAT -3'
827
866
  3'- ATGTGCCGTGTA -5'
828
867
  Imperfect DNA mirror repeats (IMRs) are less than 100% symmetrical.
829
868
  ^^^ integrate mirror repeats creation
830
869
  and searching for them. Hmmm.
831
870
  --------------------------------------------------------------------------------
832
- (129) → continue porting bioroebe/taxonomy
871
+ (128) → continue porting bioroebe/taxonomy
833
872
  ^^^^^^^^^^
834
873
  It has been 5 years ...
835
874
  ^^^ taxonomy/colours/colours wird integriert
836
875
  ^^^ das ist der nächste schritt, so das
837
876
  wir das nit mehr benötigen.
838
877
  --------------------------------------------------------------------------------
839
- (130) → find out which bacteria all contain the needle complex; find out
878
+ (129) → find out which bacteria all contain the needle complex; find out
840
879
  the sequence for the needle complex as well and study it;
841
880
  find the positions of the genes responsible.
842
881
  --------------------------------------------------------------------------------
843
- (131) → Add trypsin_digest, also in the shell, but possibly
882
+ (130) → Add trypsin_digest, also in the shell, but possibly
844
883
  on toplevel as well (if the input is a protein sequence.
845
884
  Also, more generally in the shell, add this:
846
885
  digest trypsin
@@ -850,22 +889,22 @@
850
889
  follows !!!
851
890
  ^^^ document this too into .md
852
891
  --------------------------------------------------------------------------------
853
- (132) → add codon usage in bioroebe
892
+ (131) → add codon usage in bioroebe
854
893
  --------------------------------------------------------------------------------
855
- (133) → Clone the following functionality.
894
+ (132) → Clone the following functionality.
856
895
  http://www.bioinformatics.nl/cgi-bin/emboss/help/sirna
857
896
  --------------------------------------------------------------------------------
858
- (134) → Improve the "find and scan" subsection. We must be able to find
897
+ (133) → Improve the "find and scan" subsection. We must be able to find
859
898
  subsequences; check for "matches" as well, including the bioshell.
860
899
  --------------------------------------------------------------------------------
861
- (135) → Clone the CLUSTAL format aligment.
900
+ (134) → Clone the CLUSTAL format aligment.
862
901
  --------------------------------------------------------------------------------
863
- (136) → We need to be able to load up a whole geneome into bioroebe,
902
+ (135) → We need to be able to load up a whole geneome into bioroebe,
864
903
  and then be able to manipulate it.
865
904
  ^^^ perhaps test this with some example
866
905
  data or so...
867
906
  --------------------------------------------------------------------------------
868
- (137) → Restriction enzymes:
907
+ (136) → Restriction enzymes:
869
908
  Add a subsection about restritction enzymes including
870
909
  examples, and also explain how to use this in bioroebe.
871
910
  Minute by minute...
@@ -875,7 +914,7 @@
875
914
  general, so that we can reproduce and verify the
876
915
  information there.
877
916
  --------------------------------------------------------------------------------
878
- (138) → clone pepinfo
917
+ (137) → clone pepinfo
879
918
  The program "pepinfo" plots various amino acid properties in
880
919
  parallel for an input protein sequence.
881
920
  The types of plot available are:
@@ -887,7 +926,7 @@
887
926
  Charged, Positive, Negative.
888
927
  The data are also written out to an output file.
889
928
  --------------------------------------------------------------------------------
890
- (139) → gff?
929
+ (138) → gff?
891
930
  There are 6 .gff3 files in the current directory.
892
931
  We will simply pass the first entry there into class Bioroebe::Parser::GFF.
893
932
  The accession id is `NZ_CP011602.1`.
@@ -896,39 +935,39 @@
896
935
  Bioroebe::Parser::GFF: in this file.
897
936
  ^^^ we need an analyze-mode as well.
898
937
  --------------------------------------------------------------------------------
899
- (140) → ^^^^ add the ability to
938
+ (139) → ^^^^ add the ability to
900
939
  show a ruler AND highlighting as well
901
940
  ^^^ then document it.
902
941
  --------------------------------------------------------------------------------
903
- (141) → https://github.com/bioperl/bioperl-live
942
+ (140) → https://github.com/bioperl/bioperl-live
904
943
  Look what we can take from ^^^.
905
944
  https://github.com/bioperl/bioperl-live/tree/master/examples
906
945
  --------------------------------------------------------------------------------
907
- (142) → continue biojava, and bioroebe a bit
946
+ (141) → continue biojava, and bioroebe a bit
908
947
  Ideally we should have biojava o a working point.
909
948
  --------------------------------------------------------------------------------
910
- (143) → clone the functionality found at https://web.expasy.org/protparam/
949
+ (142) → clone the functionality found at https://web.expasy.org/protparam/
911
950
  https://web.expasy.org/cgi-bin/protparam/protparam
912
951
  ^^^ this is halfway done...
913
952
  ^^^^ also add pI calculation:
914
953
  Theoretical pI: 5.78
915
954
  --------------------------------------------------------------------------------
916
- (144) → NP_417539.1
955
+ (143) → NP_417539.1
917
956
  https://www.ncbi.nlm.nih.gov/protein/NP_417539.1
918
957
  https://www.ncbi.nlm.nih.gov/protein/NP_417539.1?report=fasta
919
958
  ^^^ if the input is exactly like the above, on the first line,
920
959
  download the sequence.
921
960
  --------------------------------------------------------------------------------
922
- (145) → http://www.biostars.org/
961
+ (144) → http://www.biostars.org/
923
962
  ^^^ regularly work through this
924
963
  and try to help
925
964
  and extend bioruby at the same time.
926
965
  --------------------------------------------------------------------------------
927
- (146) → The taxonomy-submodule should work one day, and be properly
966
+ (145) → The taxonomy-submodule should work one day, and be properly
928
967
  documented as well. Perhaps integrate the parts of Taxonomy
929
968
  that can be included into the toplevel domain.
930
969
  --------------------------------------------------------------------------------
931
- (147) → Enable:
970
+ (146) → Enable:
932
971
  Bioroebe.set_genetic_code()
933
972
  Bioroebe.set_genetic_code(to: 'Vertebrate Mitochondrial')
934
973
  ^^^ enable this
@@ -939,58 +978,58 @@
939
978
  Seq('MAIVMGRWKGAR*')
940
979
  ^^^ enable this as well; extent documentation too.
941
980
  --------------------------------------------------------------------------------
942
- (148) → We have found a restriction enzyme called NheI.
981
+ (147) → We have found a restriction enzyme called NheI.
943
982
  The sequence this 6-cutter relates to is: `5' - GCTAGC - 3'`
944
983
  This restriction enzyme will produce a blunt overhang.
945
984
  ^^^ nope das ist falsch
946
985
  --------------------------------------------------------------------------------
947
- (149) → Sau3A?
986
+ (148) → Sau3A?
948
987
  ^^^ enable this restriction site
949
988
  --------------------------------------------------------------------------------
950
- (150) → Add matplotlib support.
989
+ (149) → Add matplotlib support.
951
990
  try_to_use_matplotlib
952
991
  --------------------------------------------------------------------------------
953
- (151) → https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/RESTfulAPIs.html
992
+ (150) → https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/RESTfulAPIs.html
954
993
  --------------------------------------------------------------------------------
955
- (152) → The following input:
994
+ (151) → The following input:
956
995
  downcase; orf?; seq?
957
996
  leads to strange display. Something is wrong here, must be checked.
958
997
  --------------------------------------------------------------------------------
959
- (153) → Continue with rosalind problems.
998
+ (152) → Continue with rosalind problems.
960
999
  These challenges can be found here:
961
1000
  http://rosalind.info/problems/sign/
962
1001
  Also integrate these rosalind-quizzes into bioroebe
963
1002
  when possible.
964
1003
  --------------------------------------------------------------------------------
965
- (154) → https://web.expasy.org/cgi-bin/peptide_mass/peptide-mass.pl
1004
+ (153) → https://web.expasy.org/cgi-bin/peptide_mass/peptide-mass.pl
966
1005
  ^^^ make the above usable in sinaitra as well
967
1006
  --------------------------------------------------------------------------------
968
- (155) → Integrate a way to search for commonly known promoters:
1007
+ (154) → Integrate a way to search for commonly known promoters:
969
1008
  promoters?
970
1009
  ^^^ this functionality
971
1010
  ^^^ this has to be expanded
972
1011
  and ...
973
1012
  --------------------------------------------------------------------------------
974
- (156) → Integrate:
1013
+ (155) → Integrate:
975
1014
  http://biotools.nubic.northwestern.edu/OligoCalc.html
976
1015
  --------------------------------------------------------------------------------
977
- (157) → Extend the Java part of BioRoebe systematically..
1016
+ (156) → Extend the Java part of BioRoebe systematically..
978
1017
  What should come next? Let's make a list.
979
1018
  → remove_numbers [DONE]
980
1019
  --------------------------------------------------------------------------------
981
- (158) → Study gnuplot; one day we have to draw graphs.
1020
+ (157) → Study gnuplot; one day we have to draw graphs.
982
1021
  --------------------------------------------------------------------------------
983
- (159) → Add a genome browser, both ascii without GUI and also
1022
+ (158) → Add a genome browser, both ascii without GUI and also
984
1023
  with. In ruby-gtk.
985
1024
  --------------------------------------------------------------------------------
986
- (160) → Clone the functionality of:
1025
+ (159) → Clone the functionality of:
987
1026
  http://www.biophp.org/minitools/restriction_digest/demo.php
988
1027
  --------------------------------------------------------------------------------
989
- (161) → Add the loxP sequence to readme [DONE] and explain this
1028
+ (160) → Add the loxP sequence to readme [DONE] and explain this
990
1029
  better on the main readme; and perhaps also assign
991
1030
  the sequence via the bioshell.
992
1031
  --------------------------------------------------------------------------------
993
- (162) → 33. Cephalodiscidae Mitochondrial UAA-Tyr Code (transl_table=33)
1032
+ (161) → 33. Cephalodiscidae Mitochondrial UAA-Tyr Code (transl_table=33)
994
1033
  AAs = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG
995
1034
  Starts = ---M-------*-------M---------------M---------------M------------
996
1035
  Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
@@ -999,7 +1038,7 @@
999
1038
  ^^^ add a parser, and document it, that can take this input
1000
1039
  and output the corresponding code, in a valid .yml file.
1001
1040
  --------------------------------------------------------------------------------
1002
- (163) → Add to bioroebe the ability to add cloning vectors
1041
+ (162) → Add to bioroebe the ability to add cloning vectors
1003
1042
  and molecular_weight calcuation
1004
1043
  for this
1005
1044
  and also to show the sequence of a vector
@@ -1015,19 +1054,19 @@
1015
1054
  ^^^ we also need a way to find out what resistance genes
1016
1055
  are carried there.
1017
1056
  --------------------------------------------------------------------------------
1018
- (164) → In the lambda genome sequence there are 10 EcoB and
1057
+ (163) → In the lambda genome sequence there are 10 EcoB and
1019
1058
  5 EcoK sites.
1020
1059
  ^^^ verify this too, as an example as well
1021
1060
  --------------------------------------------------------------------------------
1022
- (165) → show restriction sites, composable and compatible with
1061
+ (164) → show restriction sites, composable and compatible with
1023
1062
  serial clone ... hmm
1024
1063
  --------------------------------------------------------------------------------
1025
- (166) → enable:
1064
+ (165) → enable:
1026
1065
  BIOROEBE_USE_COLOURS:
1027
1066
  can be 0 or 1
1028
1067
  what is this?
1029
1068
  --------------------------------------------------------------------------------
1030
- (167) → Burrows-Wheeler-Transform (BWT)
1069
+ (166) → Burrows-Wheeler-Transform (BWT)
1031
1070
  ^^^ add some method here
1032
1071
  Bioroebe.burrows_wheeler_transform
1033
1072
  ^^^ if no '$' char is in the input, then append it
@@ -1037,13 +1076,13 @@
1037
1076
  also test this against my paper-result
1038
1077
  with input being: "GATAG$".
1039
1078
  --------------------------------------------------------------------------------
1040
- (168) → Enable working with several genes... hmm and store that somewhere.
1079
+ (167) → Enable working with several genes... hmm and store that somewhere.
1041
1080
  Something like a per-project workspace thingy.
1042
1081
  --------------------------------------------------------------------------------
1043
- (169) → Add:
1082
+ (168) → Add:
1044
1083
  http://nar.oxfordjournals.org/content/35/suppl_2/W71.long
1045
1084
  --------------------------------------------------------------------------------
1046
- (170) → Now, you may want to translate the nucleotides up to
1085
+ (169) → Now, you may want to translate the nucleotides up to
1047
1086
  the first in frame stop codon, and then stop (as
1048
1087
  happens in nature):
1049
1088
  coding_dna.translate()
@@ -1054,12 +1093,12 @@
1054
1093
  Then continue from here:
1055
1094
  https://people.duke.edu/~ccc14/pcfb/biopython/BiopythonSequences.html
1056
1095
  --------------------------------------------------------------------------------
1057
- (171) → Add:
1096
+ (170) → Add:
1058
1097
  set_dna :Ubiquitin
1059
1098
  set_dna :ubiquitin
1060
1099
  ^^^ we want to obtain the ubuiqitin sequence
1061
1100
  --------------------------------------------------------------------------------
1062
- (172) → Telomers
1101
+ (171) → Telomers
1063
1102
  Telomeres are listed from 5' to 3'.
1064
1103
  Example for the human telomeres would be:
1065
1104
  5'-TTAGGG-3
@@ -1068,25 +1107,25 @@
1068
1107
  doc_telomeres
1069
1108
  ^^^ add this to say the human telomere sequence
1070
1109
  --------------------------------------------------------------------------------
1071
- (173) → ORF_positions?
1110
+ (172) → ORF_positions?
1072
1111
  ^^^ change this a bit, to actually show the positions
1073
1112
  of the various ORFs with the start-position.
1074
1113
  --------------------------------------------------------------------------------
1075
- (174) → add:
1114
+ (173) → add:
1076
1115
  setgene2
1077
1116
  add_dna2
1078
1117
  dna2
1079
1118
  dna? <--- this one is not a setter but a query.
1080
1119
  --------------------------------------------------------------------------------
1081
- (175) → improve the TM calculation. must be better, must have more
1120
+ (174) → improve the TM calculation. must be better, must have more
1082
1121
  documentation, and a small tutorial.
1083
1122
  --------------------------------------------------------------------------------
1084
- (176) → Compare bioroebe to:
1123
+ (175) → Compare bioroebe to:
1085
1124
  https://www.ncbi.nlm.nih.gov/orffinder
1086
1125
  whether both return the same
1087
1126
  also possibly add a web-gui
1088
1127
  --------------------------------------------------------------------------------
1089
- (177) → Find out ratios from:
1128
+ (176) → Find out ratios from:
1090
1129
  Doolittle RF. 1989. Redundancies in protein sequences. I
1091
1130
  http://onlinelibrary.wiley.com/doi/10.1110/ps.9.6.1203/pdf
1092
1131
  ^^^ that table perhaps
@@ -1105,33 +1144,33 @@
1105
1144
  Bioroebe::Blosum[50] as an API.
1106
1145
  and document it in general.
1107
1146
  --------------------------------------------------------------------------------
1108
- (178) → http://www.biomart.org/other/user-docs.pdf
1147
+ (177) → http://www.biomart.org/other/user-docs.pdf
1109
1148
  ^^^ work through this
1110
1149
  --------------------------------------------------------------------------------
1111
- (179) → add:
1150
+ (178) → add:
1112
1151
  class Cell
1113
1152
  ^^^ simulate a cell
1114
1153
  Hmmm. Needs specific components ... and needs a better plan.
1115
1154
  --------------------------------------------------------------------------------
1116
- (180) → class Protein:
1155
+ (179) → class Protein:
1117
1156
  add glycosyslation patteren
1118
1157
  .glycosylated? yes no
1119
1158
  + glycoslated?
1120
1159
  need to somehow add the modiication type
1121
1160
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358406/
1122
1161
  --------------------------------------------------------------------------------
1123
- (181) → In the BioShell we must be able to do probes - completementary
1162
+ (180) → In the BioShell we must be able to do probes - completementary
1124
1163
  to amino acids.
1125
1164
  --------------------------------------------------------------------------------
1126
- (182) → Add www-related functionality to bioroebe eventually make use
1165
+ (181) → Add www-related functionality to bioroebe eventually make use
1127
1166
  of rails, but start with sinatra possibly. In the long run,
1128
1167
  make it flexible to work with as many different frameworks
1129
1168
  as possible, though.
1130
1169
  --------------------------------------------------------------------------------
1131
- (183) → Spaltstellen anzeigen zum beispiel lambda-DNA verdau
1170
+ (182) → Spaltstellen anzeigen zum beispiel lambda-DNA verdau
1132
1171
  BgI II.
1133
1172
  --------------------------------------------------------------------------------
1134
- (184) → dnaanalyze
1173
+ (183) → dnaanalyze
1135
1174
  In the DNA string `TCCGTCGCAACACATCGCCTCAACAAACCGACCGGGATATGCAATACCGGAATCCGATCCTTTAGAAGCTGCATTCCAAACGCTTGCAATAACACCCACTCGACTATTCAGCATTGGCAAAGGGTACGAATTCGACGAAGGGAGGGTGCTATATTTTCCAAGTTGCTCGCCGATTGATACGGAGCCTGTGGAAAGATTTCGCGGCTCTAGTCTTTAGCTTTGATGTCACCCCTGAGTAGTAACCCGGCGTGGTAGCTTTCATTAGACTTCTCGGAGAGAGTATTAAGCAAAGGTGGAGGTCCCAGGGGTCCAGTGAGCTGTATCGCACTAAAAGCATGCCTACGGGCAATGCTATTTTGCTCACAGGAACTTTGGGGGAGCCACAAACTCTCGAAGCCGGATTGTTGTGGCGGCTAACTTTCCAAAGGCGACCATTCATGGTCTGAATGGGCCCTCACCAGAAGAACGTTTTCGACGGGCATTCTTCCCCGGGGTTTCGAAGGCAAGGGTCAGCACGGCGCGGAAAAGTACGCGACGCATACCGGACTAGTCATGCAACTCCCTCGGAACTGGCGATTCCCACCCAAGAGACGCACGCTGATCATTGCCCATGCCGACTGGAGATGCTGAATTTGGTATGCGGGTCTGTTGCCAGCGCTGACATTATCGGACATTGTGGGGAGAACCGTGTGATTGATTGAGCTGGCGCATTTGTCCGCATGCTCTCCTCATGTGGACACCTTCGCAGGTTCTTTCCGCGGCCACAGTGTCGGGATCTACCCCTGGTGCGTCGCCGCGAGTACAGGTGGGGTTTCGCGCATGAGAACCAATGTTGCACGCCTCAAAACATGGCTGTAACATATTAGCGCCAATAAAAATTTTTGGCAACAAAGAAACAAGGCCAACCGAAGTGCTAAGCCGCGATCATGAAGGGGCGATGCCAGAATGGGAGTCTGCCTTTCCTGTGTGGACGTGAGATTGTACCTAGACAGAGAACGCC` we found these Nucleotides:
1136
1175
  ================================================================================
1137
1176
  Adenines: 244 | 24.40 %
@@ -1150,11 +1189,11 @@
1150
1189
  can be assigned, and dnaanalyse --GUI should
1151
1190
  start it too. ALSO document it once this works.
1152
1191
  --------------------------------------------------------------------------------
1153
- (185) → go through the individual components slowly and improve them,
1192
+ (184) → go through the individual components slowly and improve them,
1154
1193
  step by step, including the documentation. Then eventually
1155
1194
  remove this todo-entry here.
1156
1195
  --------------------------------------------------------------------------------
1157
- (186) → Add a consensus sequence for:
1196
+ (185) → Add a consensus sequence for:
1158
1197
  Asn-X-Ser/Thr-Conesnsus
1159
1198
  first in a yaml file; also documented, then also add
1160
1199
  a way to scan for these something like:
@@ -1164,7 +1203,7 @@
1164
1203
  /N-?Glyc/i
1165
1204
  ^^^ use that regex
1166
1205
  --------------------------------------------------------------------------------
1167
- (187) → require 'bio'
1206
+ (186) → require 'bio'
1168
1207
  # creating a Bio::Sequence::NA object containing ambiguous alphabets
1169
1208
  ambiguous_seq = Bio::Sequence::NA.new("atgcyrwskmbdhvn")
1170
1209
  # show the contents and class of the DNA sequence object
@@ -1181,31 +1220,31 @@
1181
1220
  so taht it can be used by both the .cgi and
1182
1221
  well rdoc...
1183
1222
  --------------------------------------------------------------------------------
1184
- (188) → Add more protein-specific thingies to bioroebe.
1223
+ (187) → Add more protein-specific thingies to bioroebe.
1185
1224
  --------------------------------------------------------------------------------
1186
- (189) → Die bioshell vorantreiben und durch std_biology.rb abarbeiten.
1225
+ (188) → Die bioshell vorantreiben und durch std_biology.rb abarbeiten.
1187
1226
  Vielleicht können wir ja etwas davon auslagern in eine Klasse
1188
1227
  oder so.
1189
1228
  Das ganze sollte auch mit Webmin (biomin) verknüpft werden, so das
1190
1229
  wir die Bioshell auch elegant über das www verwenden können!
1191
1230
  --------------------------------------------------------------------------------
1192
- (190) → ^^^ when we find restriction enzyme sites in a DNA
1231
+ (189) → ^^^ when we find restriction enzyme sites in a DNA
1193
1232
  string, colourize them RED.
1194
1233
  also set it to
1195
1234
  set_restriction_size()
1196
1235
  --------------------------------------------------------------------------------
1197
- (191) → also ... while learning C++ we extend the project here...
1236
+ (190) → also ... while learning C++ we extend the project here...
1198
1237
  Useful C++ things will be combined.
1199
1238
  --------------------------------------------------------------------------------
1200
- (192) → As of April 2003, there were 176,890 total taxa represented.
1239
+ (191) → As of April 2003, there were 176,890 total taxa represented.
1201
1240
  ^^^ we need a way to also output how many entries we
1202
1241
  have there.
1203
1242
  --------------------------------------------------------------------------------
1204
- (193) → Replace bioruby with bioroebe completely!
1243
+ (192) → Replace bioruby with bioroebe completely!
1205
1244
  In order for this to work, we first need to find out
1206
1245
  what bioruby is able to do. :P
1207
1246
  --------------------------------------------------------------------------------
1208
- (194) → append 33
1247
+ (193) → append 33
1209
1248
  # ^^^ in the bioshell
1210
1249
  Only numbers were given: Adding 33 random nucleotides to the main string next.
1211
1250
  Traceback (most recent call last):
@@ -1223,7 +1262,7 @@
1223
1262
  Did you mean? return_random_codon_sequence_for_this_aminoacid_sequence
1224
1263
  ^^^^^ BUG!
1225
1264
  --------------------------------------------------------------------------------
1226
- (195) → > rest?
1265
+ (194) → > rest?
1227
1266
  We found these restriction sites within the sequence `TTCAGAACTCAACGCCTGGTTGGCCGTCCAGTAAGCTGACTAAGTAAGTCTATGCCCGCGATAACCAGGATACAGATATCGTGAAACCTGGTTTATCTCCTTCTATAAGAGTCTGCACATCTAGC`:
1228
1267
  AccII → CGCG ( 1 times found)
1229
1268
  AluI → AGCT ( 1 times found)
@@ -1233,22 +1272,22 @@
1233
1272
  BshFI → GGCC ( 1 times found)
1234
1273
  BstFNI → CGCG ( 1 times found)
1235
1274
  BstUI → CGCG ( 1 times found)
1236
- BsuRI -> GGCC ( 1 times found)
1237
- CviRI -> TGCA ( 1 times found)
1238
- Eco32I -> GATATC ( 1 times found)
1239
- EcoRV -> GATATC ( 1 times found)
1240
- FnuDII -> CGCG ( 1 times found)
1241
- HaeIII -> GGCC ( 1 times found)
1242
- HpyCH4V -> TGCA ( 1 times found)
1243
- MaeI -> CTAG ( 1 times found)
1244
- MvnI -> CGCG ( 1 times found)
1245
- PalI -> GGCC ( 1 times found)
1246
- SelI -> CGCG ( 1 times found)
1247
- ThaI -> CGCG ( 1 times found)
1275
+ BsuRI → GGCC ( 1 times found)
1276
+ CviRI → TGCA ( 1 times found)
1277
+ Eco32I → GATATC ( 1 times found)
1278
+ EcoRV → GATATC ( 1 times found)
1279
+ FnuDII → CGCG ( 1 times found)
1280
+ HaeIII → GGCC ( 1 times found)
1281
+ HpyCH4V → TGCA ( 1 times found)
1282
+ MaeI → CTAG ( 1 times found)
1283
+ MvnI → CGCG ( 1 times found)
1284
+ PalI → GGCC ( 1 times found)
1285
+ SelI → CGCG ( 1 times found)
1286
+ ThaI → CGCG ( 1 times found)
1248
1287
  XspI → CTAG ( 1 times found)
1249
1288
  ^^^^ also show the position
1250
1289
  --------------------------------------------------------------------------------
1251
- (196) → PMID entries are:
1290
+ (195) → PMID entries are:
1252
1291
  x = 'Goldman, JM, Melo JV 2003 NEJM 349:1451 14534339
1253
1292
  Lewis GD 1993 Cancer Immunol Immun other 37: 255 8102322
1254
1293
  McShane LM 2009 Clin Canc Res 15: 1898 19276274
@@ -1303,13 +1342,13 @@
1303
1342
  ^^^ enable this... but I am not sure what is meant with
1304
1343
  that. :\
1305
1344
  --------------------------------------------------------------------------------
1306
- (197) → Bei der Datenbanksuche werden die gemessenen Massen mit den Peptidmassen
1345
+ (196) → Bei der Datenbanksuche werden die gemessenen Massen mit den Peptidmassen
1307
1346
  aller Proteine bzw. Gene in einer Datenbank (NCBI, Uniprot) verglichen. DNA-
1308
1347
  Sequenzen werden dazu in Proteinsequenzen übersetzt und in silico mit der beim
1309
1348
  Verdau benutzten Protease geschnitten.
1310
1349
  ^^^ enable digestions
1311
1350
  --------------------------------------------------------------------------------
1312
- (198) → Complexity of libraries:
1351
+ (197) → Complexity of libraries:
1313
1352
  How many independent clones are necessary to represent a genome (plant,
1314
1353
  animal/fungus) or how many such clones have to be screened to have realistic
1315
1354
  chance of finding the gene of interest?
@@ -1339,7 +1378,7 @@
1339
1378
  Most plants have reasonable genome size (e.g. tomato about 800 Mb) - 15 filters
1340
1379
  have to be hybridized.
1341
1380
  --------------------------------------------------------------------------------
1342
- (199) → BIO SHELL> BglI?
1381
+ (198) → BIO SHELL> BglI?
1343
1382
  We have found a restriction enzyme called BglI.
1344
1383
  The sequence this 11-cutter relates to is: `5' - GCCNNNNNGGC - 3'`
1345
1384
  It will specifically cut between: 5' - GCCNNNN|NGGC - 3'
@@ -1368,12 +1407,12 @@
1368
1407
  List all enzymes that produce compatible ends for the enzyme.
1369
1408
  http://biopython.org/DIST/docs/api/Bio.Restriction.Restriction.Blunt-class.html
1370
1409
  --------------------------------------------------------------------------------
1371
- (200) → https://www.reddit.com/r/bioinformatics/comments/5o3kn8/bioinformatics_contest_2017_jan_23rd29th_solve_as/
1410
+ (199) → https://www.reddit.com/r/bioinformatics/comments/5o3kn8/bioinformatics_contest_2017_jan_23rd29th_solve_as/
1372
1411
  --------------------------------------------------------------------------------
1373
- (201) → Finish all of biophp integration into bioroebe.
1412
+ (200) → Finish all of biophp integration into bioroebe.
1374
1413
  http://www.biophp.org/
1375
1414
  --------------------------------------------------------------------------------
1376
- (202) → locate oriC here:
1415
+ (201) → locate oriC here:
1377
1416
  ttcgttaagtaacttcactgcccgtagtgtaccggcattcgctagcaagagtctttctg
1378
1417
  ggcaagcttcacttgtgatcgcggcctgtgcccccggaatgaaacaaccacgtccctgct
1379
1418
  aacaacgacgggaaaagggaagtgatccgtcggcagacccagactagtgcccttctccgg
@@ -1394,17 +1433,17 @@
1394
1433
  ^^^ these give us slices
1395
1434
  But I do not know how to locate ORIs.
1396
1435
  --------------------------------------------------------------------------------
1397
- (203) → ^^^ also integrate git into bioroebe.
1436
+ (202) → ^^^ also integrate git into bioroebe.
1398
1437
  --------------------------------------------------------------------------------
1399
- (204) → WIR MÜSSEN DAS HIER EXTREM VERBESSERN.
1438
+ (203) → WIR MÜSSEN DAS HIER EXTREM VERBESSERN.
1400
1439
  DANN UPLOADEN UND ALS BASIS FÜR APPLICATIONS NUTZEN.
1401
1440
  --------------------------------------------------------------------------------
1402
- (205) → Study MetaCyc
1441
+ (204) → Study MetaCyc
1403
1442
  ^^^ study metabolic pathways.
1404
1443
  http://metacyc.org/
1405
1444
  → Create KuroMetaCyc, in Analogy towards Metabolic Cycle.
1406
1445
  --------------------------------------------------------------------------------
1407
- (206) → Welcome to BioShell May 2012. Type "help" to get some help.
1446
+ (205) → Welcome to BioShell May 2012. Type "help" to get some help.
1408
1447
  Hello and welcome to the Bio Shell Version, last updated: May 2012
1409
1448
  BIO SHELL> IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI
1410
1449
  BIO SHELL> HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA
@@ -1418,7 +1457,7 @@
1418
1457
  When we type this, we then ask:
1419
1458
  "Please input your FASTA format now:"
1420
1459
  --------------------------------------------------------------------------------
1421
- (207) → http://biopython.org/DIST/docs/cookbook/Restriction.html#mozTocId101269
1460
+ (206) → http://biopython.org/DIST/docs/cookbook/Restriction.html#mozTocId101269
1422
1461
  ^^^ support this also:
1423
1462
  >>> from Bio import Restriction
1424
1463
  >>> dir()
@@ -1474,15 +1513,15 @@
1474
1513
  test.xmd
1475
1514
  /home/kumar/Desktop/test_exit/InputMicrographs/
1476
1515
  --------------------------------------------------------------------------------
1477
- (208) → BioTodo - GENESIS, science fiction.
1516
+ (207) → BioTodo - GENESIS, science fiction.
1478
1517
  - create virus(:which_one, :amount) # Note the difference to the below
1479
1518
  - create hydra(:amount)
1480
1519
  - create bread
1481
1520
  --------------------------------------------------------------------------------
1482
- (209) → both
1521
+ (208) → both
1483
1522
  ^ should work, does not work right now.
1484
1523
  --------------------------------------------------------------------------------
1485
- (210) → Taxonomy is now integrated into bioroebe. This is good but we need more
1524
+ (209) → Taxonomy is now integrated into bioroebe. This is good but we need more
1486
1525
  documentation, some more tests, a rethinking of the layout and the
1487
1526
  structures, and a fixing of the query-part of the database.
1488
1527
  Also, make sure that it does the main functions.
@@ -1494,12 +1533,12 @@
1494
1533
  AND document this related-problems too
1495
1534
  Integrate this some other day...
1496
1535
  --------------------------------------------------------------------------------
1497
- (211) → http://www.restrictionmapper.org/cgi-bin/sitefind3.pl
1536
+ (210) → http://www.restrictionmapper.org/cgi-bin/sitefind3.pl
1498
1537
  ^^^ Das sollte man integrieren, die Funktionalität, so das
1499
1538
  man ALLE Restriktion-Enzymes ausprobiert ausgehend von
1500
1539
  einer bestimmten Sequenz.
1501
1540
  --------------------------------------------------------------------------------
1502
- (212) → A search is essentially substring search across a database of strings
1541
+ (211) → A search is essentially substring search across a database of strings
1503
1542
  (albeit with a smaller alphabet). Some common use cases: one,
1504
1543
  scientists will search for certain genes that they've used in engineered
1505
1544
  plasmids. Two, since multiple codons can translate to the same amino
@@ -1515,13 +1554,13 @@
1515
1554
  Bioroebe::DetermineOptimalCodons
1516
1555
  ^^^ this is currently incomplete.
1517
1556
  --------------------------------------------------------------------------------
1518
- (213) → Redo restrictions enzymes completely.
1557
+ (212) → Redo restrictions enzymes completely.
1519
1558
  And polish this a LOT.
1520
1559
  This may take some days. But we want this to be REALLY good and
1521
1560
  lasting for a long time.
1522
1561
  Need to keep on working at that!
1523
1562
  --------------------------------------------------------------------------------
1524
- (214) → Add: average_aminoacid_weight?
1563
+ (213) → Add: average_aminoacid_weight?
1525
1564
  → === LV-Nummer 300214 UE Übung III B Sequenzanalysen in der Molekularbiologie
1526
1565
  → Pubmed
1527
1566
  → Finding sequences
@@ -1556,7 +1595,7 @@
1556
1595
  But where is the alignment comparer? perhaps hamming distance?
1557
1596
  hmm we have to see.
1558
1597
  --------------------------------------------------------------------------------
1559
- (215) → /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/menu.rb:311:in `menu': undefined method `upcase' for ["EcoRI"]:Array (NoMethodError)
1598
+ (214) → /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/menu.rb:311:in `menu': undefined method `upcase' for ["EcoRI"]:Array (NoMethodError)
1560
1599
  from /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/user_input.rb:31:in `block in enter_main_loop'
1561
1600
  from /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/user_input.rb:12:in `loop'
1562
1601
  from /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/user_input.rb:12:in `enter_main_loop'
@@ -1578,10 +1617,10 @@
1578
1617
  at this date.'
1579
1618
  SendEmail.new to: Roebe.email?, data
1580
1619
  --------------------------------------------------------------------------------
1581
- (216) → Document which parts of emboss have already been copied.
1620
+ (215) → Document which parts of emboss have already been copied.
1582
1621
  → EMBOSS.md
1583
1622
  --------------------------------------------------------------------------------
1584
- (217) → Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta
1623
+ (216) → Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta
1585
1624
  Bioroebe::Shell: Now loading from `Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta`.
1586
1625
  Bioroebe::ParseFasta: Will read from the file `Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta`.
1587
1626
  This sequence is assumed to be DNA or RNA.
@@ -1622,7 +1661,7 @@
1622
1661
  - Learn from:
1623
1662
  http://www.snapgene.com/products/snapgene_viewer/
1624
1663
  --------------------------------------------------------------------------------
1625
- (218) → Wir sollten GFP tagging unterstützen, also wie das
1664
+ (217) → Wir sollten GFP tagging unterstützen, also wie das
1626
1665
  Protein-Konstrukt aussehen soll und so weiter.
1627
1666
  Das geht teilweise...
1628
1667
  GFP? zeigt die Sequenz an.
@@ -1631,21 +1670,21 @@
1631
1670
  Was fehlt? Hmmmm... eventuell noch mehr an
1632
1671
  dokumentation.
1633
1672
  --------------------------------------------------------------------------------
1634
- (219) → in bioroebe, create subsequences for siRNA, then scan for
1673
+ (218) → in bioroebe, create subsequences for siRNA, then scan for
1635
1674
  submatcher + report where these are. Should be fast too.
1636
1675
  --------------------------------------------------------------------------------
1637
- (220) → Reverse complement now works quite well, also via the sinatra
1676
+ (219) → Reverse complement now works quite well, also via the sinatra
1638
1677
  interface. We still should have a way to show 5' and
1639
1678
  3', both on the commandline, and via sinatra.
1640
1679
  Perhaps via --fancy commandline flag or so.
1641
1680
  --------------------------------------------------------------------------------
1642
- (221) → Cn3D files?
1681
+ (220) → Cn3D files?
1643
1682
  ^^^ add support for these; research what they are, too.
1644
1683
  --------------------------------------------------------------------------------
1645
- (222) → Consider adding graphviz, perhaps to the taxonomy project
1684
+ (221) → Consider adding graphviz, perhaps to the taxonomy project
1646
1685
  where we make graphs towards different nodes or so...
1647
1686
  --------------------------------------------------------------------------------
1648
- (223) → in parse fasta
1687
+ (222) → in parse fasta
1649
1688
  @colourize_sequence = false
1650
1689
  ^^^ change this lateron...
1651
1690
  perhaps create a toplevel method
@@ -1653,7 +1692,7 @@
1653
1692
  the check better whether it is a protein or a DNA/RNA
1654
1693
  add a toplevel method for this.
1655
1694
  --------------------------------------------------------------------------------
1656
- (224) → clone the BLast ident matcher functionality for aminacids into
1695
+ (223) → clone the BLast ident matcher functionality for aminacids into
1657
1696
  Bioroebe.
1658
1697
  - fasta_download AAC76198.2
1659
1698
  ^^^ enable the above in the bioshell, and perhaps also outside
@@ -1661,7 +1700,7 @@
1661
1700
  http://www.ncbi.nlm.nih.gov/protein/145693187?report=fasta
1662
1701
  ^^^ shall use something such as the above
1663
1702
  --------------------------------------------------------------------------------
1664
- (225) → Be able to mark exon/intron boundaries.
1703
+ (224) → Be able to mark exon/intron boundaries.
1665
1704
  - Add "taxid?" to tell us the name of the organism. This works now.
1666
1705
  ^^^ should also work with a local database. ← we integrate this
1667
1706
  at a later point.
@@ -1693,15 +1732,15 @@
1693
1732
  ^^^
1694
1733
  study sumoplot ...
1695
1734
  --------------------------------------------------------------------------------
1696
- (226) → http://a-little-book-of-r-for-bioinformatics.readthedocs.io/en/latest/src/chapter7.html
1735
+ (225) → http://a-little-book-of-r-for-bioinformatics.readthedocs.io/en/latest/src/chapter7.html
1697
1736
  --------------------------------------------------------------------------------
1698
- (227) → http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc22
1737
+ (226) → http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc22
1699
1738
  ^^^ continue here; "You can also specify the table using the
1700
1739
  NCBI table number which is shorter, and often included in
1701
1740
  the feature annotation of GenBank files:"
1702
1741
  ^^^ work through this and see if it is good.
1703
1742
  --------------------------------------------------------------------------------
1704
- (228) → Clone ALL of biophp, if it us useful.
1743
+ (227) → Clone ALL of biophp, if it us useful.
1705
1744
  Then state so too, then get rid of this entry here.
1706
1745
  But remember, we must also be able to do so via a webinterface!
1707
1746
  Oligos now work. Hmm.
@@ -1734,7 +1773,7 @@
1734
1773
  We should also put this poart into doc/ subsection
1735
1774
  to keep track of what is missing and what is not.
1736
1775
  --------------------------------------------------------------------------------
1737
- (229) → sizeseq
1776
+ (228) → sizeseq
1738
1777
  ^^^ clone this functionality and describe it in detail.
1739
1778
  also for the www. Hmmm. Need to add this for the
1740
1779
  www.
@@ -1764,7 +1803,7 @@
1764
1803
  ^^^ demonstrate via foobar.fasta
1765
1804
  ALSO ADD A GUI; sizeseq.rb was added in February 2021.
1766
1805
  --------------------------------------------------------------------------------
1767
- (230) → In the sinatra-web-interface for Bioroebe:
1806
+ (229) → In the sinatra-web-interface for Bioroebe:
1768
1807
  continue quiz in rosalind !!!
1769
1808
  also, at to_dna: default to RNA
1770
1809
  And improve the general quality.
@@ -1783,9 +1822,9 @@
1783
1822
  111^^^^ in ncbi format
1784
1823
  and document all of this.
1785
1824
  --------------------------------------------------------------------------------
1786
- (231) →
1825
+ (230) →
1787
1826
  --------------------------------------------------------------------------------
1788
- (232) → Add a ruby-GUI stuff, probably the old biology/ subsection
1827
+ (231) → Add a ruby-GUI stuff, probably the old biology/ subsection
1789
1828
  will be moved into the project.
1790
1829
  Also tell how to start or get this GUI stuff to run, then add
1791
1830
  components that can be a part of bioroebe into it.
@@ -1795,7 +1834,7 @@
1795
1834
  ^^^ implement smith waterman alignment
1796
1835
  swalign AAGGGGAGGACGATGCGGATGTTC AGGGAGGACGATGCGG
1797
1836
  --------------------------------------------------------------------------------
1798
- (233) → Query: cmdline (16 nt)
1837
+ (232) → Query: cmdline (16 nt)
1799
1838
  Ref : cmdline (24 nt)
1800
1839
  Query: 1 A-GGGAGGACGATGCGG 16
1801
1840
  | |||||||||||||||
@@ -1805,7 +1844,7 @@
1805
1844
  Mismatches: 1
1806
1845
  CIGAR: 1M1D15M
1807
1846
  --------------------------------------------------------------------------------
1808
- (234) → ^^^^ also add this commandline tool
1847
+ (233) → ^^^^ also add this commandline tool
1809
1848
  bin/swalin
1810
1849
  should have same output
1811
1850
  - Gene finding in genomes
@@ -1841,7 +1880,7 @@
1841
1880
  puts seq1.to_fasta("testseq", 60)
1842
1881
  ^^^^ enable this
1843
1882
  --------------------------------------------------------------------------------
1844
- (235) → Identifying amino acid cleavage sites (Sigcleave)
1883
+ (234) → Identifying amino acid cleavage sites (Sigcleave)
1845
1884
  For amino acid sequences we may be interested to know whether
1846
1885
  the amino acid sequence contains a cleavable signal sequence
1847
1886
  for directing the transport of the protein within the cell.
@@ -1860,15 +1899,15 @@
1860
1899
  to the output of the original sigcleave utility.
1861
1900
  The syntax for using Sigcleave is as follows:
1862
1901
  # create a Seq object, for example:
1863
- $seqobj = Bio::Seq->new(-seq => "AALLHHHHHHGGGGPPRTTTTTVVVVVVVVVVVVVVV");
1902
+ $seqobj = Bio::Seq→new(-seq => "AALLHHHHHHGGGGPPRTTTTTVVVVVVVVVVVVVVV");
1864
1903
  use Bio::Tools::Sigcleave;
1865
1904
  $sigcleave_object = new Bio::Tools::Sigcleave
1866
1905
  ( -seq => $seqobj,
1867
1906
  -threshold => 3.5,
1868
1907
  -description => 'test sigcleave protein seq',
1869
1908
  );
1870
- %raw_results = $sigcleave_object->signals;
1871
- $formatted_output = $sigcleave_object->pretty_print;
1909
+ %raw_results = $sigcleave_object→signals;
1910
+ $formatted_output = $sigcleave_object→pretty_print;
1872
1911
  Please see Bio::Tools::Sigcleave for details.
1873
1912
  ^^^ add this
1874
1913
  http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Tools/Sigcleave.html
@@ -1891,15 +1930,15 @@
1891
1930
  Which one specifically? Let's see...
1892
1931
  https://www.expasy.org/
1893
1932
  --------------------------------------------------------------------------------
1894
- (236) → https://biopython.org/wiki/Category%3ACookbook
1933
+ (235) → https://biopython.org/wiki/Category%3ACookbook
1895
1934
  ^^^ clone that
1896
1935
  --------------------------------------------------------------------------------
1897
- (237) → include covid genome, and begin to analyse it in bioroebe
1936
+ (236) → include covid genome, and begin to analyse it in bioroebe
1898
1937
  "Das Genom von SARS-CoV-2 sei doppelt so groß wie jenes
1899
1938
  von Influenzaviren, daher scheinen letztere viermal
1900
1939
  so schnell zu mutieren, schrieb Moshiri."
1901
1940
  --------------------------------------------------------------------------------
1902
- (238) → Look at the GUIs that are part of the BioRoebe project.
1941
+ (237) → Look at the GUIs that are part of the BioRoebe project.
1903
1942
  Polish these part, at the least one widget, then
1904
1943
  make a screenshot, as the first one.
1905
1944
  Then upload the image + new release and docu!
@@ -1911,14 +1950,14 @@
1911
1950
  Hmmm. And then, also consider transitioning into gtk3,
1912
1951
  and make mroe screenshots.
1913
1952
  --------------------------------------------------------------------------------
1914
- (239) → https://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/
1953
+ (238) → https://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/
1915
1954
  http://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=emboss_pepstats-I20160208-020243-0564-53154194-oy
1916
1955
  ^^^^ clone the pepstat functionality
1917
1956
  printAA RLAVQYAPLSGCHSTIREDVHNLHFCRARKE*
1918
1957
  - Improve on temperature content and how it is calculated
1919
1958
  someone googled for it in 2014 so build on it
1920
1959
  --------------------------------------------------------------------------------
1921
- (240) → pfasta /Depot/Temp/bioroebe/NM_000539.3_Homo_sapiens_rhodopsin_RHO.fasta
1960
+ (239) → pfasta /Depot/Temp/bioroebe/NM_000539.3_Homo_sapiens_rhodopsin_RHO.fasta
1922
1961
  Will read from the file `/Depot/Temp/bioroebe/NM_000539.3_Homo_sapiens_rhodopsin_RHO.fasta`.
1923
1962
  Bioroebe::ParseFasta: This sequence is assumed to be a protein.
1924
1963
  This sequence has 2768 aminoacids.
@@ -1928,7 +1967,7 @@
1928
1967
  AGAGTCATCCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAG
1929
1968
  AGAGTCATCCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAG
1930
1969
  --------------------------------------------------------------------------------
1931
- (241) → Formats
1970
+ (240) → Formats
1932
1971
  BioPerl's SeqIO system understands lot of formats and can interconvert
1933
1972
  all of them. Here is a current listing of formats, as of version 1.6.
1934
1973
  ^^^ must implement this too
@@ -1976,10 +2015,10 @@
1976
2015
  tinyseq NCBI TinySeq XML
1977
2016
  ztr ZTR tracefile ztr
1978
2017
  --------------------------------------------------------------------------------
1979
- (242) → Look at f1 display:
2018
+ (241) → Look at f1 display:
1980
2019
  10 20 30 40 50 60 70 80 90 100
1981
2020
  --------------------------------------------------------------------------------
1982
- (243) → 1 ATGCAGTTACTTCGCTGTTTTTCAATATTTTCTGTTATTGCTTCAGTTTTAGCACAGGAACTGACAACTATATGCGAGCAAATCCCCTCACCAACTTTAG 100
2021
+ (242) → 1 ATGCAGTTACTTCGCTGTTTTTCAATATTTTCTGTTATTGCTTCAGTTTTAGCACAGGAACTGACAACTATATGCGAGCAAATCCCCTCACCAACTTTAG 100
1983
2022
  F1 1 M Q L L R C F S I F S V I A S V L A Q E L T T I C E Q I P S P T L E 34
1984
2023
  ^^^ when we do f1
1985
2024
  the aminoacid sequence position is on the next
@@ -1991,7 +2030,7 @@
1991
2030
  BEFORE we add ANY COLOURS.
1992
2031
  OH WELL.
1993
2032
  --------------------------------------------------------------------------------
1994
- (244) → Add a primer-design widget
2033
+ (243) → Add a primer-design widget
1995
2034
  The idea is to be able to manipulate forward and
1996
2035
  reverse primer areas.
1997
2036
  AND research how to do this ...
@@ -2001,7 +2040,7 @@
2001
2040
  ^^^ and check what is useful there. perhaps also add
2002
2041
  nicer visual cues to pretty it up a bit.
2003
2042
  --------------------------------------------------------------------------------
2004
- (245) → Compare bioroebe to:
2043
+ (244) → Compare bioroebe to:
2005
2044
  https://www.ncbi.nlm.nih.gov/orffinder
2006
2045
  whether both return the same also possibly add a web-gui
2007
2046
  → it must also allow for different tables to be used!
@@ -2009,18 +2048,18 @@
2009
2048
  but also in different ORFs
2010
2049
  und die länge angeben, zumindest vom längsten ORF start + stop... also so das das ergebnis auch passt
2011
2050
  --------------------------------------------------------------------------------
2012
- (246) → test reverse complement in bioroebe
2051
+ (245) → test reverse complement in bioroebe
2013
2052
  ^^^
2014
2053
  new_WWW/
2015
2054
  ^^^ this should eventually become the new web-related interface.
2016
2055
  Ah well. Perhaps not ... ruby-cgi is soooooo annoying ...
2017
2056
  --------------------------------------------------------------------------------
2018
- (247) → the blosum-viewer should be supported in the cgi part
2057
+ (246) → the blosum-viewer should be supported in the cgi part
2019
2058
  and sinatra part as well.
2020
2059
  This now works for sinatra. Need to enable this for
2021
2060
  the cgi-part too eventually.
2022
2061
  --------------------------------------------------------------------------------
2023
- (248) → port the sinatra stuff together in bioroebe
2062
+ (247) → port the sinatra stuff together in bioroebe
2024
2063
  create a dir: web_api
2025
2064
  ^^^ also make params? usable in both sinatra and cgi page
2026
2065
  well ...............
@@ -2031,47 +2070,47 @@
2031
2070
  and replace the ad-hoc code otherwise...
2032
2071
  ^^^ yeah, finish the HtmlTemplate stuff.
2033
2072
  --------------------------------------------------------------------------------
2034
- (249) → https://i.imgur.com/ptcSn12.png
2073
+ (248) → https://i.imgur.com/ptcSn12.png
2035
2074
  ^^^ enable such an overview; this shows mass compuation e.g
2036
2075
  peptide mass and such
2037
2076
  --------------------------------------------------------------------------------
2038
- (250) → Bioroebe.sanitize_nucleotide_sequence
2077
+ (249) → Bioroebe.sanitize_nucleotide_sequence
2039
2078
  ^^^ port this into java. The code has been written for this already,
2040
2079
  but we currently fail to link it.
2041
2080
  --------------------------------------------------------------------------------
2042
- (251) → Batch-create the .exe files on windows for libui, once
2081
+ (250) → Batch-create the .exe files on windows for libui, once
2043
2082
  the first has been added. And then test it too
2044
2083
  AND document it. This should be done with the controller
2045
2084
  eventually. Once this works, we can remove this entry
2046
2085
  here.
2047
2086
  --------------------------------------------------------------------------------
2048
- (252) → port more libui stuff in bioroebe. We have two widgets ported so far;
2087
+ (251) → port more libui stuff in bioroebe. We have two widgets ported so far;
2049
2088
  add more such entries.
2050
2089
  --------------------------------------------------------------------------------
2051
- (253) → after libui has been ported, explore how gosu works on windows.
2090
+ (252) → after libui has been ported, explore how gosu works on windows.
2052
2091
  if possible add things to a gosu-specific UI as well, but
2053
2092
  we may need a common, unified GUI base for that.
2054
2093
  --------------------------------------------------------------------------------
2055
- (254) → (86)
2094
+ (253) → (86)
2056
2095
  add libui bindings AND once done make sure the controller works in
2057
2096
  libui as well. Embed the various things into it.
2058
2097
  Tab A set named tabs for placing items in
2059
2098
  ^^^ use this perhaps also in bioroebe hmmm
2060
2099
  yeah.
2061
2100
  --------------------------------------------------------------------------------
2062
- (255) → https://github.com/cnjinhao/nana/wiki/User-Works-using-Nana
2101
+ (254) → https://github.com/cnjinhao/nana/wiki/User-Works-using-Nana
2063
2102
  ^^^ port the "DNA hybrid"
2064
2103
  https://camo.githubusercontent.com/4c27d554ca4d698d288628f21255f917c2c577e35d7e11dd67e21880d56b6b0a/687474703a2f2f6e616e6170726f2e6f72672f696d616765732f73637265656e73686f74732f746864795f7365715f6578706c2e706e67
2065
2104
  --------------------------------------------------------------------------------
2066
- (256) → Bioroebe::Cell
2105
+ (255) → Bioroebe::Cell
2067
2106
  ^^^ think about what to do with it. If we don't need it then perhaps
2068
2107
  we should just remove it. Think about this more at 2022, before
2069
2108
  deciding what to do.
2070
2109
  --------------------------------------------------------------------------------
2071
- (257) → Add emboss cgplot functionality.
2110
+ (256) → Add emboss cgplot functionality.
2072
2111
  https://www.bioinformatics.nl/cgi-bin/emboss/cpgplot
2073
2112
  --------------------------------------------------------------------------------
2074
- (258) → integrate calculation of the Instability index (II)
2113
+ (257) → integrate calculation of the Instability index (II)
2075
2114
  The instability index provides an estimate of the
2076
2115
  stability of your protein in a test tube. Statistical
2077
2116
  analysis of 12 unstable and 32 stable proteins has
@@ -2096,14 +2135,14 @@
2096
2135
  The instability index (II) is computed to be 65.43
2097
2136
  This classifies the protein as unstable.
2098
2137
  --------------------------------------------------------------------------------
2099
- (259) → We have now added a method to show all hydrophobic amino acids, via the
2138
+ (258) → We have now added a method to show all hydrophobic amino acids, via the
2100
2139
  method .hydrophobic_amino_acids?. This works and has been documented
2101
2140
  in May 2022. However had, we also still need a way to PREDICT
2102
2141
  hydrophobic segments in a polypeptide sequence.
2103
2142
  --------------------------------------------------------------------------------
2104
- (260) → <img src="https://i.imgur.com/tkB8MTJ.png" style="margin: 1em">
2143
+ (259) → <img src="https://i.imgur.com/tkB8MTJ.png" style="margin: 1em">
2105
2144
  --------------------------------------------------------------------------------
2106
- (261) → https://www.studocu.com/en-us/document/queens-college-cuny/biochemistry-laboratory/bioinformatics-exercise/13329106
2145
+ (260) → https://www.studocu.com/en-us/document/queens-college-cuny/biochemistry-laboratory/bioinformatics-exercise/13329106
2107
2146
  ^^^ this enable via a method
2108
2147
  and add a screenshot
2109
2148
  we want to colourize an existing string
@@ -2115,7 +2154,7 @@
2115
2154
  However had, we should add a sinatra demo app too,
2116
2155
  and demonstrate this too and then documen it as-is
2117
2156
  --------------------------------------------------------------------------------
2118
- (262) →
2157
+ (261) →
2119
2158
  make sure we have a good fasta-showing widget
2120
2159
  show how many nucleotides are
2121
2160
  AND add support to modify this as-is
@@ -2127,7 +2166,7 @@
2127
2166
  or something ... perhaps also keybindings by default
2128
2167
  and a help option somewhere to explain all of this.
2129
2168
  --------------------------------------------------------------------------------
2130
- (263) → Add a way in bioroebe to store a gene into a yaml file
2169
+ (262) → Add a way in bioroebe to store a gene into a yaml file
2131
2170
  or so, and to also load it up again. Perhaps simplify
2132
2171
  this automatically. Need some ways to describe that.
2133
2172
  FastaToYaml
@@ -2136,55 +2175,55 @@
2136
2175
  This class now exists. We have to add more features to it
2137
2176
  eventually, though.
2138
2177
  --------------------------------------------------------------------------------
2139
- (264) → https://pubchem.ncbi.nlm.nih.gov/compound/16131099#section=Top
2178
+ (263) → https://pubchem.ncbi.nlm.nih.gov/compound/16131099#section=Top
2140
2179
  ^^^ this website is quite interesting; try to use components
2141
2180
  from it.
2142
2181
  --------------------------------------------------------------------------------
2143
- (265) → Add some option to show the aminoacid sequence, at the least
2182
+ (264) → Add some option to show the aminoacid sequence, at the least
2144
2183
  store it; and optionally show it.
2145
2184
  possibly always report how many aminoacids are
2146
2185
  part of that file; and optionally also show
2147
2186
  the whole sequence.
2148
2187
  --------------------------------------------------------------------------------
2149
- (266) → http://insilico.ehu.es/
2188
+ (265) → http://insilico.ehu.es/
2150
2189
  ^^^ check if we have all of this incorporated
2151
2190
  --------------------------------------------------------------------------------
2152
- (267) → Integrate these nice GUI parts parts:
2191
+ (266) → Integrate these nice GUI parts parts:
2153
2192
  https://dev.to/kojix2/introduction-to-gr-rb-data-visualization-with-ruby-2c39
2154
2193
  --------------------------------------------------------------------------------
2155
- (268) → AND THEN test on windows as well.
2194
+ (267) → AND THEN test on windows as well.
2156
2195
  ^^^^^^^^^^^^^^
2157
2196
  --------------------------------------------------------------------------------
2158
- (269) → add mouse chromsoome URL, also in the bioshell
2197
+ (268) → add mouse chromsoome URL, also in the bioshell
2159
2198
  and the main README, to be of help for the
2160
2199
  user. add a mouse subsection.
2161
2200
  --------------------------------------------------------------------------------
2162
- (270) → fix the taxonomy stuff...
2201
+ (269) → fix the taxonomy stuff...
2163
2202
  --------------------------------------------------------------------------------
2164
- (271) → set_dna_sequence alu
2203
+ (270) → set_dna_sequence alu
2165
2204
  ^^^ fetch random alu
2166
2205
  ^^^ alu sequence
2167
2206
  Ok we started this now adding more details, but we
2168
2207
  need to become better at searching for this
2169
2208
  sequence.
2170
2209
  --------------------------------------------------------------------------------
2171
- (272) → draw things based on GR
2210
+ (271) → draw things based on GR
2172
2211
  --------------------------------------------------------------------------------
2173
- (273) → https://mycocosm.jgi.doe.gov/help/screenshots/browser_viewer.png
2212
+ (272) → https://mycocosm.jgi.doe.gov/help/screenshots/browser_viewer.png
2174
2213
  ^^^ offer the same functionality
2175
2214
  --------------------------------------------------------------------------------
2176
- (274) → https://genome.cshlp.org/content/12/10/1611/F3.expansion.html
2215
+ (273) → https://genome.cshlp.org/content/12/10/1611/F3.expansion.html
2177
2216
  ^^^ enable this, we must obtain a sequence then store into genbank format
2178
2217
  so, first fetch; then store as-is.
2179
2218
  --------------------------------------------------------------------------------
2180
- (275) → be able to generate nice graphics
2219
+ (274) → be able to generate nice graphics
2181
2220
  https://genome.cshlp.org/content/12/10/1611/F1.large.jpg
2182
2221
  --------------------------------------------------------------------------------
2183
- (276) → add rmagicks wrappre, perhaps via imageparadise or something
2222
+ (275) → add rmagicks wrappre, perhaps via imageparadise or something
2184
2223
  the idea is that we can make fancy drawings and generate
2185
2224
  an image for the end user to see
2186
2225
  --------------------------------------------------------------------------------
2187
- (277) → https://bioperl.org/howtos/Beginners_HOWTO.html#item13
2226
+ (276) → https://bioperl.org/howtos/Beginners_HOWTO.html#item13
2188
2227
  extend the sequence object and document it
2189
2228
  also add:
2190
2229
  class Genome
@@ -2196,7 +2235,7 @@
2196
2235
  @internal_hash[:species] # return the species here
2197
2236
  end
2198
2237
  --------------------------------------------------------------------------------
2199
- (278) → http://lib.ysu.am/open_books/312400.pdf
2238
+ (277) → http://lib.ysu.am/open_books/312400.pdf
2200
2239
  clone:
2201
2240
  Primer.pl
2202
2241
  This program was written to support the required informatics for a sequencing
@@ -2219,23 +2258,23 @@
2219
2258
  of the program lie in the classes and the methods we call. The next section
2220
2259
  examines the Primer3 module, which is similar to many Bioperl modules
2221
2260
  --------------------------------------------------------------------------------
2222
- (279) → Clone all of Emboss. :)
2261
+ (278) → Clone all of Emboss. :)
2223
2262
  → Clone and document the getorf functionality properly.
2224
2263
  See: http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html
2225
2264
  http://emboss.sourceforge.net
2226
2265
  http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html
2227
2266
  --------------------------------------------------------------------------------
2228
- (280) → Add useful formulas for bioshell.
2267
+ (279) → Add useful formulas for bioshell.
2229
2268
  --------------------------------------------------------------------------------
2230
- (281) → Polish the GUI sets:
2269
+ (280) → Polish the GUI sets:
2231
2270
  https://i.imgur.com/djElIMh.png
2232
2271
  --------------------------------------------------------------------------------
2233
- (282) → The taxonomy part should be fully integrated, without it
2272
+ (281) → The taxonomy part should be fully integrated, without it
2234
2273
  being a standalone part anymore.
2235
2274
  continue on the taxonomy stuff.
2236
2275
  ne day this will work again *shake fist*
2237
2276
  --------------------------------------------------------------------------------
2238
- (283) → Show the frequency of codons in different tables
2277
+ (282) → Show the frequency of codons in different tables
2239
2278
  This works quite ok, but right now the approach is to store
2240
2279
  this in a .yml file which is not ideal.
2241
2280
  Thus, we have to add two things:
@@ -2246,14 +2285,14 @@
2246
2285
  Add where this can be found.
2247
2286
  IMPROVE THIS ALL!!!!!!!
2248
2287
  --------------------------------------------------------------------------------
2249
- (284) → improve docu + tests for melting temperature analysis again
2288
+ (283) → improve docu + tests for melting temperature analysis again
2250
2289
  + usage example + GUI + web-use
2251
2290
  --------------------------------------------------------------------------------
2252
- (285) → https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec15
2291
+ (284) → https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec15
2253
2292
  ^^^ work through the above, also integrate it + write docs
2254
2293
  https://raw.githubusercontent.com/biopython/biopython/master/Doc/examples/ls_orchid.fasta
2255
2294
  --------------------------------------------------------------------------------
2256
- (286) → work a bit more on tk!!!
2295
+ (285) → work a bit more on tk!!!
2257
2296
  in particular to start it from the bioshell as-is.
2258
2297
  ^^^ this is mostly done for quick
2259
2298
  demonstration purposes
@@ -2264,15 +2303,18 @@
2264
2303
  protein_to_DNA
2265
2304
  ^^^^ improve both while improving tk_paradise docu as well.
2266
2305
  --------------------------------------------------------------------------------
2267
- (287) → add 2nd_orf
2306
+ (286) → add 2nd_orf
2268
2307
  → this shall scan for the 2nd orf
2269
2308
  → and third ORF as well, then, and document it.
2270
2309
  --------------------------------------------------------------------------------
2271
- (288) → https://github.com/pjotrp/bigbio
2310
+ (287) → https://github.com/pjotrp/bigbio
2272
2311
  ^^^^ include uses cases from that readme
2273
2312
  --------------------------------------------------------------------------------
2274
- (289) -> bioinformatiocs bioroebe:
2275
- cut_via(:trypsin)
2276
- ^^^^ show the digest as array
2277
- then upload after documenting this
2278
- ------------------------------------------------------------------------
2313
+ (288) → bioinformatiocs bioroebe:
2314
+ cut_via(:trypsin)
2315
+ ^^^^ show the digest as array
2316
+ then upload after documenting this
2317
+ --------------------------------------------------------------------------------
2318
+ (289) -> we need to be able to draw graphical elements such as a bar
2319
+ with an arrow, representing DNA.
2320
+