bioroebe 0.10.80

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Files changed (802) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.md +428 -0
  3. data/README.md +9280 -0
  4. data/bin/advanced_dotplot +7 -0
  5. data/bin/align_open_reading_frames +12 -0
  6. data/bin/all_positions_of_this_nucleotide +7 -0
  7. data/bin/aminoacid_composition +7 -0
  8. data/bin/aminoacid_frequencies +12 -0
  9. data/bin/aminoacid_substitution +7 -0
  10. data/bin/automatically_rename_this_fasta_file +7 -0
  11. data/bin/base_composition +7 -0
  12. data/bin/batch_create_windows_executables +7 -0
  13. data/bin/biomart_console +11 -0
  14. data/bin/bioroebe +27 -0
  15. data/bin/bioroebe_controller +10 -0
  16. data/bin/bioshell +26 -0
  17. data/bin/blosum_2D_table +12 -0
  18. data/bin/calculate_n50_value +12 -0
  19. data/bin/chunked_display +12 -0
  20. data/bin/codon_frequency +9 -0
  21. data/bin/codon_to_aminoacid +30 -0
  22. data/bin/colourize_this_fasta_sequence +14 -0
  23. data/bin/compact_fasta_file +7 -0
  24. data/bin/complement +7 -0
  25. data/bin/complementary_dna_strand +12 -0
  26. data/bin/complementary_rna_strand +12 -0
  27. data/bin/compseq +7 -0
  28. data/bin/consensus_sequence +17 -0
  29. data/bin/count_AT +12 -0
  30. data/bin/count_GC +12 -0
  31. data/bin/create_random_aminoacids +7 -0
  32. data/bin/decode_this_aminoacid_sequence +20 -0
  33. data/bin/deduce_aminoacid_sequence +13 -0
  34. data/bin/deduce_most_likely_aminoacid_sequence +7 -0
  35. data/bin/display_aminoacid_table +12 -0
  36. data/bin/display_open_reading_frames +7 -0
  37. data/bin/dna_to_aminoacid_sequence +7 -0
  38. data/bin/dna_to_rna +7 -0
  39. data/bin/downcase_chunked_display +12 -0
  40. data/bin/download_this_pdb +7 -0
  41. data/bin/fasta_index +7 -0
  42. data/bin/fetch_data_from_uniprot +12 -0
  43. data/bin/filter_away_invalid_nucleotides +12 -0
  44. data/bin/find_substring +19 -0
  45. data/bin/genbank_to_fasta +7 -0
  46. data/bin/hamming_distance +12 -0
  47. data/bin/input_as_dna +12 -0
  48. data/bin/is_palindrome +13 -0
  49. data/bin/leading_five_prime +7 -0
  50. data/bin/levensthein +7 -0
  51. data/bin/longest_ORF +14 -0
  52. data/bin/longest_substring +12 -0
  53. data/bin/n_stop_codons_in_this_sequence +15 -0
  54. data/bin/open_reading_frames +14 -0
  55. data/bin/overwrite_fasta_header +7 -0
  56. data/bin/palindrome_2D_structure +7 -0
  57. data/bin/palindrome_generator +7 -0
  58. data/bin/parse_fasta +7 -0
  59. data/bin/partner_nucleotide +9 -0
  60. data/bin/possible_codons_for_this_aminoacid +12 -0
  61. data/bin/random_dna_sequence +12 -0
  62. data/bin/random_sequence +12 -0
  63. data/bin/raw_hamming_distance +12 -0
  64. data/bin/return_longest_substring_via_LCS_algorithm +7 -0
  65. data/bin/reverse_complement +7 -0
  66. data/bin/reverse_sequence +7 -0
  67. data/bin/ruler +12 -0
  68. data/bin/scan_this_input_for_startcodons +12 -0
  69. data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
  70. data/bin/show_atomic_composition +7 -0
  71. data/bin/show_codon_usage +12 -0
  72. data/bin/show_fasta_header +7 -0
  73. data/bin/show_nucleotide_sequence +7 -0
  74. data/bin/show_this_codon_table +7 -0
  75. data/bin/show_this_dna_sequence +7 -0
  76. data/bin/showorf +14 -0
  77. data/bin/simplify_fasta +7 -0
  78. data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
  79. data/bin/split_this_fasta_file_into_chromosomes +7 -0
  80. data/bin/strict_filter_away_invalid_aminoacids +7 -0
  81. data/bin/taxonomy +63 -0
  82. data/bin/three_to_one +7 -0
  83. data/bin/to_rna +7 -0
  84. data/bin/trailing_three_prime +7 -0
  85. data/bin/trypsin_digest +7 -0
  86. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
  87. data/bioroebe.gemspec +97 -0
  88. data/doc/IUPAC_aminoacids_code.md +36 -0
  89. data/doc/IUPAC_nucleotide_code.md +19 -0
  90. data/doc/README.gen +9237 -0
  91. data/doc/blosum.md +5 -0
  92. data/doc/compatibility/BIO_PHP.md +37 -0
  93. data/doc/compatibility/README.md +3 -0
  94. data/doc/compatibility/emboss.md +56 -0
  95. data/doc/extensive_usage_example.md +35 -0
  96. data/doc/german_names_for_the_aminoacids.md +27 -0
  97. data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
  98. data/doc/legacy_paths.md +9 -0
  99. data/doc/pdb_ATOM_entry.md +33 -0
  100. data/doc/quality_control/README.md +2 -0
  101. data/doc/quality_control/commandline_applications.md +13 -0
  102. data/doc/resources.md +23 -0
  103. data/doc/setup.rb +1655 -0
  104. data/doc/statistics/statistics.md +41 -0
  105. data/doc/todo/README.md +5 -0
  106. data/doc/todo/bioroebe_GUI_todo.md +15 -0
  107. data/doc/todo/bioroebe_todo.md +2823 -0
  108. data/doc/using_biomart.md +258 -0
  109. data/html/test.html +144 -0
  110. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
  111. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
  112. data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
  113. data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
  114. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
  115. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
  116. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
  117. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
  118. data/lib/bioroebe/annotations/README.md +2 -0
  119. data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
  120. data/lib/bioroebe/autoinclude.rb +7 -0
  121. data/lib/bioroebe/base/base.rb +35 -0
  122. data/lib/bioroebe/base/colours.rb +14 -0
  123. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
  124. data/lib/bioroebe/base/commandline_application/README.md +7 -0
  125. data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
  126. data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
  127. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
  128. data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
  129. data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
  130. data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
  131. data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
  132. data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
  133. data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
  134. data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
  135. data/lib/bioroebe/base/initialize.rb +18 -0
  136. data/lib/bioroebe/base/misc.rb +94 -0
  137. data/lib/bioroebe/base/namespace.rb +16 -0
  138. data/lib/bioroebe/base/prototype/README.md +12 -0
  139. data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
  140. data/lib/bioroebe/base/prototype/misc.rb +108 -0
  141. data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
  142. data/lib/bioroebe/base/prototype/prototype.rb +21 -0
  143. data/lib/bioroebe/base/prototype/reset.rb +26 -0
  144. data/lib/bioroebe/base/reset.rb +11 -0
  145. data/lib/bioroebe/biomart/LICENSE.md +27 -0
  146. data/lib/bioroebe/biomart/attribute.rb +77 -0
  147. data/lib/bioroebe/biomart/biomart.rb +227 -0
  148. data/lib/bioroebe/biomart/database.rb +128 -0
  149. data/lib/bioroebe/biomart/dataset.rb +572 -0
  150. data/lib/bioroebe/biomart/filter.rb +97 -0
  151. data/lib/bioroebe/biomart/server.rb +152 -0
  152. data/lib/bioroebe/blosum/blosum.rb +88 -0
  153. data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
  154. data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
  155. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
  156. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
  157. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
  158. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
  159. data/lib/bioroebe/cell/README.md +1 -0
  160. data/lib/bioroebe/cell/cell.rb +63 -0
  161. data/lib/bioroebe/cleave_and_digest/README.md +2 -0
  162. data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
  163. data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
  164. data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
  165. data/lib/bioroebe/codon_tables/README.md +9 -0
  166. data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
  167. data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
  168. data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
  169. data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
  170. data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
  171. data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
  172. data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
  173. data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
  174. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
  175. data/lib/bioroebe/codons/README.md +28 -0
  176. data/lib/bioroebe/codons/codon_table.rb +416 -0
  177. data/lib/bioroebe/codons/codon_tables.rb +123 -0
  178. data/lib/bioroebe/codons/codons.rb +517 -0
  179. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
  180. data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
  181. data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
  182. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
  183. data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
  184. data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
  185. data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
  186. data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
  187. data/lib/bioroebe/codons/start_codons.rb +105 -0
  188. data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
  189. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
  190. data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
  191. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
  192. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
  193. data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
  194. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
  195. data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
  196. data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
  197. data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
  198. data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
  199. data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
  200. data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
  201. data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
  202. data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
  203. data/lib/bioroebe/colours/colours.rb +119 -0
  204. data/lib/bioroebe/colours/misc_colours.rb +80 -0
  205. data/lib/bioroebe/colours/rev.rb +41 -0
  206. data/lib/bioroebe/colours/sdir.rb +21 -0
  207. data/lib/bioroebe/colours/sfancy.rb +21 -0
  208. data/lib/bioroebe/colours/sfile.rb +21 -0
  209. data/lib/bioroebe/colours/simp.rb +21 -0
  210. data/lib/bioroebe/colours/swarn.rb +29 -0
  211. data/lib/bioroebe/colours/use_colours.rb +27 -0
  212. data/lib/bioroebe/configuration/configuration.rb +114 -0
  213. data/lib/bioroebe/configuration/constants.rb +35 -0
  214. data/lib/bioroebe/constants/GUIs.rb +79 -0
  215. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
  216. data/lib/bioroebe/constants/base_directory.rb +120 -0
  217. data/lib/bioroebe/constants/carriage_return.rb +14 -0
  218. data/lib/bioroebe/constants/codon_tables.rb +77 -0
  219. data/lib/bioroebe/constants/database_constants.rb +107 -0
  220. data/lib/bioroebe/constants/files_and_directories.rb +579 -0
  221. data/lib/bioroebe/constants/misc.rb +189 -0
  222. data/lib/bioroebe/constants/newline.rb +14 -0
  223. data/lib/bioroebe/constants/nucleotides.rb +114 -0
  224. data/lib/bioroebe/constants/regex.rb +28 -0
  225. data/lib/bioroebe/constants/roebe.rb +38 -0
  226. data/lib/bioroebe/constants/row_terminator.rb +16 -0
  227. data/lib/bioroebe/constants/tabulator.rb +14 -0
  228. data/lib/bioroebe/constants/unicode.rb +12 -0
  229. data/lib/bioroebe/constants/urls.rb +50 -0
  230. data/lib/bioroebe/conversions/README.md +3 -0
  231. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
  232. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
  233. data/lib/bioroebe/count/README.md +1 -0
  234. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
  235. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
  236. data/lib/bioroebe/count/count_at.rb +39 -0
  237. data/lib/bioroebe/count/count_gc.rb +43 -0
  238. data/lib/bioroebe/css/README.md +5 -0
  239. data/lib/bioroebe/css/project.css +121 -0
  240. data/lib/bioroebe/data/README.md +10 -0
  241. data/lib/bioroebe/data/bam/README.md +1 -0
  242. data/lib/bioroebe/data/data.txt +192 -0
  243. data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
  244. data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
  245. data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
  246. data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
  247. data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
  248. data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
  249. data/lib/bioroebe/data/fasta/test.fasta +7 -0
  250. data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
  251. data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
  252. data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
  253. data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
  254. data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
  255. data/lib/bioroebe/data/genbank/standard.fasta +3 -0
  256. data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
  257. data/lib/bioroebe/data/gff/sample.gff +2 -0
  258. data/lib/bioroebe/data/gff/test_gene.gff +4 -0
  259. data/lib/bioroebe/data/gff/transcripts.gff +16 -0
  260. data/lib/bioroebe/data/gtf/README.md +1 -0
  261. data/lib/bioroebe/data/json/example_config.json +48 -0
  262. data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
  263. data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
  264. data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
  265. data/lib/bioroebe/data/phylip/README.md +11 -0
  266. data/lib/bioroebe/data/phylip/example.phylip +7 -0
  267. data/lib/bioroebe/data/svg/example.svg +301 -0
  268. data/lib/bioroebe/databases/README.md +1 -0
  269. data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
  270. data/lib/bioroebe/dotplots/README.md +5 -0
  271. data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
  272. data/lib/bioroebe/dotplots/dotplot.rb +184 -0
  273. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
  274. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
  275. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
  276. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
  277. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
  278. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
  279. data/lib/bioroebe/encoding/README.md +2 -0
  280. data/lib/bioroebe/encoding/encoding.rb +45 -0
  281. data/lib/bioroebe/enzymes/README.md +2 -0
  282. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
  283. data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
  284. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
  285. data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
  286. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
  287. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
  288. data/lib/bioroebe/exceptions/README.md +2 -0
  289. data/lib/bioroebe/exceptions/exceptions.rb +17 -0
  290. data/lib/bioroebe/ext/LICENCE.md +5 -0
  291. data/lib/bioroebe/ext/README.md +7 -0
  292. data/lib/bioroebe/ext/main.cpp +45 -0
  293. data/lib/bioroebe/ext/nucleotide.cpp +24 -0
  294. data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
  295. data/lib/bioroebe/ext/sequence +0 -0
  296. data/lib/bioroebe/ext/sequence.cpp +162 -0
  297. data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
  298. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
  299. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
  300. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
  301. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
  302. data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
  303. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
  304. data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
  305. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
  306. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
  307. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
  308. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
  309. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
  310. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
  311. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
  312. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
  313. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
  314. data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
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  577. data/lib/bioroebe/svg/track.rb +263 -0
  578. data/lib/bioroebe/taxonomy/README.md +1 -0
  579. data/lib/bioroebe/taxonomy/chart.rb +95 -0
  580. data/lib/bioroebe/taxonomy/class_methods.rb +181 -0
  581. data/lib/bioroebe/taxonomy/colours.rb +26 -0
  582. data/lib/bioroebe/taxonomy/constants.rb +218 -0
  583. data/lib/bioroebe/taxonomy/edit.rb +97 -0
  584. data/lib/bioroebe/taxonomy/help/help.rb +65 -0
  585. data/lib/bioroebe/taxonomy/help/helpline.rb +53 -0
  586. data/lib/bioroebe/taxonomy/info/check_available.rb +143 -0
  587. data/lib/bioroebe/taxonomy/info/info.rb +337 -0
  588. data/lib/bioroebe/taxonomy/info/is_dna.rb +150 -0
  589. data/lib/bioroebe/taxonomy/interactive.rb +1933 -0
  590. data/lib/bioroebe/taxonomy/menu.rb +905 -0
  591. data/lib/bioroebe/taxonomy/node.rb +118 -0
  592. data/lib/bioroebe/taxonomy/parse_fasta.rb +383 -0
  593. data/lib/bioroebe/taxonomy/shared.rb +287 -0
  594. data/lib/bioroebe/taxonomy/taxonomy.rb +521 -0
  595. data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +56 -0
  596. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +715 -0
  597. data/lib/bioroebe/toplevel_methods/atomic_composition.rb +198 -0
  598. data/lib/bioroebe/toplevel_methods/base_composition.rb +121 -0
  599. data/lib/bioroebe/toplevel_methods/blast.rb +153 -0
  600. data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
  601. data/lib/bioroebe/toplevel_methods/cat.rb +71 -0
  602. data/lib/bioroebe/toplevel_methods/chunked_display.rb +92 -0
  603. data/lib/bioroebe/toplevel_methods/cliner.rb +81 -0
  604. data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
  605. data/lib/bioroebe/toplevel_methods/convert_global_env.rb +39 -0
  606. data/lib/bioroebe/toplevel_methods/databases.rb +73 -0
  607. data/lib/bioroebe/toplevel_methods/delimiter.rb +19 -0
  608. data/lib/bioroebe/toplevel_methods/digest.rb +71 -0
  609. data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +146 -0
  610. data/lib/bioroebe/toplevel_methods/e.rb +20 -0
  611. data/lib/bioroebe/toplevel_methods/editor.rb +21 -0
  612. data/lib/bioroebe/toplevel_methods/esystem.rb +22 -0
  613. data/lib/bioroebe/toplevel_methods/exponential_growth.rb +74 -0
  614. data/lib/bioroebe/toplevel_methods/extract.rb +56 -0
  615. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +353 -0
  616. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +257 -0
  617. data/lib/bioroebe/toplevel_methods/frequencies.rb +92 -0
  618. data/lib/bioroebe/toplevel_methods/hamming_distance.rb +60 -0
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  620. data/lib/bioroebe/toplevel_methods/is_on_roebe.rb +39 -0
  621. data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
  622. data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
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  624. data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
  625. data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
  626. data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
  627. data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
  628. data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
  629. data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
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  633. data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
  634. data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
  635. data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
  636. data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
  637. data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
  638. data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
  639. data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
  640. data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
  641. data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
  642. data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
  643. data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
  644. data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
  645. data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
  646. data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
  647. data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
  648. data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
  649. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
  650. data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
  651. data/lib/bioroebe/toplevel_methods/url.rb +36 -0
  652. data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
  653. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
  654. data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
  655. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
  656. data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
  657. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
  658. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
  659. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
  660. data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
  661. data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
  662. data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
  663. data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
  664. data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
  665. data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
  666. data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
  667. data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
  668. data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
  669. data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
  670. data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
  671. data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
  672. data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
  673. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
  674. data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
  675. data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
  676. data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
  677. data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
  678. data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
  679. data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
  680. data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
  681. data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
  682. data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
  683. data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
  684. data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
  685. data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
  686. data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
  687. data/lib/bioroebe/version/version.rb +44 -0
  688. data/lib/bioroebe/viennarna/README.md +3 -0
  689. data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
  690. data/lib/bioroebe/with_gui.rb +18 -0
  691. data/lib/bioroebe/www/bioroebe.cgi +44 -0
  692. data/lib/bioroebe/www/embeddable_interface.rb +686 -0
  693. data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
  694. data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
  695. data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
  696. data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
  697. data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
  698. data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
  699. data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
  700. data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
  701. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
  702. data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
  703. data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
  704. data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
  705. data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
  706. data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
  707. data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
  708. data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
  709. data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
  710. data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
  711. data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
  712. data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
  713. data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
  714. data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
  715. data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
  716. data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
  717. data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
  718. data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
  719. data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
  720. data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
  721. data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
  722. data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
  723. data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
  724. data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
  725. data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
  726. data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
  727. data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
  728. data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
  729. data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
  730. data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
  731. data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
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  733. data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
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  735. data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
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  737. data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
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  740. data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
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  748. data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
  749. data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
  750. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
  751. data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
  752. data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
  753. data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
  754. data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
  755. data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
  756. data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
  757. data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
  758. data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
  759. data/lib/bioroebe/yaml/genomes/README.md +16 -0
  760. data/lib/bioroebe/yaml/humans/README.md +2 -0
  761. data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
  762. data/lib/bioroebe/yaml/laboratory/README.md +1 -0
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  765. data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
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  767. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
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  772. data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
  773. data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
  774. data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
  775. data/lib/bioroebe/yaml/primers/README.md +4 -0
  776. data/lib/bioroebe/yaml/primers/primers.yml +3 -0
  777. data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
  778. data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
  779. data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
  780. data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
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  782. data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
  783. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
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  785. data/lib/bioroebe/yaml/sequences/README.md +2 -0
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  790. data/spec/testing_toplevel_method_editor.rb +20 -0
  791. data/spec/testing_toplevel_method_url.rb +15 -0
  792. data/spec/testing_toplevel_method_verbose.rb +13 -0
  793. data/test/advanced_svg_example.rb +307 -0
  794. data/test/testing_bioroebe.rb +25 -0
  795. data/test/testing_codons.rb +45 -0
  796. data/test/testing_dna_to_rna_conversion.rb +15 -0
  797. data/test/testing_parse_pdb_file.rb +23 -0
  798. data/test/testing_reverse_complement.rb +32 -0
  799. data/test/testing_svg_component_of_bioroebe.rb +311 -0
  800. data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
  801. data/test/testing_taxonomy.rb +22 -0
  802. metadata +1059 -0
data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml ADDED
@@ -0,0 +1,630 @@
1
+ # =========================================================================== #
2
+ # === restriction_enzymes.yml
3
+ #
4
+ # Restriction enzymes:
5
+ #
6
+ # This file contains different restriction enzymes. It may contain ONLY
7
+ # restriction enzymes, no other enzyme type.
8
+ #
9
+ # In german the name is "Restriktionsenzyme". There are currently 530
10
+ # of them listed in this file here. (We do have 533, but I assume that
11
+ # 3 may be duplicates - not entirely sure.)
12
+ #
13
+ # If you see an entry such as AGGCCT, then this is actually a shorter
14
+ # variant representing 5' AGGCCT.
15
+ #
16
+ # To update to the latest, one should use the latest enzyme list from REBASE:
17
+ #
18
+ # http://rebase.neb.com/rebase/
19
+ # http://rebase.neb.com/rebase/link_bairochc
20
+ #
21
+ # Always note down the latest version of REBASE here, which can be obtained
22
+ # from the following link:
23
+ #
24
+ # http://rebase.neb.com/rebase/NEWS.html
25
+ #
26
+ # REBASE: Version 106, May 30 2021
27
+ #
28
+ # The target sequence may include a '/' character. This is used by some
29
+ # websites, such as:
30
+ #
31
+ # https://international.neb.com/tools-and-resources/selection-charts/alphabetized-list-of-recognition-specificities
32
+ #
33
+ # =========================================================================== #
34
+ # x = YAML.load_file(Bioroebe.file_restriction_enzymes)
35
+ # x = YAML.load_file(Bioroebe.file_restriction_enzymes).keys.size
36
+ # =========================================================================== #
37
+ # Name: Sequence
38
+ # =========================================================================== #
39
+
40
+ # =========================================================================== #
41
+ # === a tig
42
+ # =========================================================================== #
43
+ AasI: GACNNNNNNGTC 7
44
+ AatI: AGGCCT 3 #
45
+ AatII: GACGTC 5
46
+ AauI: TGTACA 1
47
+ AccI: GTMKAC 2
48
+ AccII: CGCG 2
49
+ AccIII: TCCGGA 1
50
+ Acc16I: TGCGCA 3
51
+ Acc65I: GGTACC 1
52
+ Acc113I: AGTACT 3
53
+ AccB1I: GGYRCC 1
54
+ AccB7I: CCANNNNNTGG 7
55
+ AclI: AACGTT 2
56
+ AcsI: RAATTY 1
57
+ AcvI: CACGTG 3
58
+ AcyI: GRCGYC 2
59
+ AdeI: CACNNNGTG 6
60
+ AfaI: GTAC 2
61
+ AfeI: AGCGCT 3
62
+ AflI: GGWCC 1
63
+ AflII: CTTAAG 1
64
+ AflIII: ACRYGT 1
65
+ AgeI: ACCGGT 1
66
+ AhaIII: TTTAAA 3
67
+ AhdI: GACNNNNNGTC 6
68
+ AhlI: ACTAGT 1
69
+ AleI: CACNNNNGTG 5
70
+ AluI: AGCT 2
71
+ Alw21I: GWGCWC 5
72
+ Alw44I: GTGCAC 1
73
+ AlwNI: CAGNNNCTG 6
74
+ Ama87I: CYCGRG 1
75
+ AocI: CCTNAGG 2
76
+ Aor51HI: AGCGCT 3
77
+ ApaI: GGGCCC 5
78
+ ApaBI: GCANNNNNTGC 8
79
+ ApaLI: GTGCAC 1
80
+ ApoI: RAATTY 1
81
+ AscI: GG/CGCGCC 2
82
+ AseI: ATTAAT 2
83
+ AsiAI: ACCGGT 1
84
+ AsiSI: GCGATCGC 5
85
+ AsnI: ATTAAT 2
86
+ AspI: GACNNNGTC 4
87
+ Asp700I: GAANNNNTTC 5
88
+ Asp718I: GGTACC 1
89
+ AspEI: GACNNNNNGTC 6
90
+ AspHI: GWGCWC 5
91
+ AspLEI: GCGC 3
92
+ AspS9I: GGNCC 1
93
+ AsuI: GGNCC 1
94
+ AsuII: TTCGAA 2
95
+ AsuC2I: CCSGG 2
96
+ AsuNHI: GCTAGC 1
97
+ AvaI: CYCGRG 1
98
+ AvaII: GGWCC 1
99
+ AviII: TGCGCA 3
100
+ AvrII: CCTAGG 1
101
+ AxyI: CCTNAGG 2
102
+
103
+ # =========================================================================== #
104
+ # === b tig
105
+ # =========================================================================== #
106
+ BsaI: GGTCTC(1/5) # URL: https://www.neb.com/tools-and-resources/selection-charts/enzymes-with-nonpalindromic-sequences
107
+ BalI: TGGCCA 3
108
+ BamHI: GGATCC 1
109
+ BanI: GGYRCC 1
110
+ BanII: GRGCYC 5
111
+ BanIII: ATCGAT 2
112
+ BbeI: GGCGCC 5
113
+ BbrPI: CACGTG 3
114
+ BbuI: GCATGC 5
115
+ Bbv12I: GWGCWC 5
116
+ BclI: TGATCA 1
117
+ BcnI: CCSGG 2
118
+ BcoI: CYCGRG 1
119
+ BcuI: ACTAGT 1
120
+ BetI: WCCGGW 1
121
+ BfaI: CTAG 1
122
+ BfmI: CTRYAG 1
123
+ BfrI: CTTAAG 1
124
+ BfrBI: ATGCAT 3
125
+ BfuCI: GATC 0
126
+ BglI: GCCNNNNNGGC 7
127
+ BglII: AGATCT 1
128
+ BlnI: CCTAGG 1
129
+ BloHII: CTGCAG 5
130
+ BlpI: GCTNAGC 2
131
+ Bme18I: GGWCC 1
132
+ Bme1390I: CCNGG 2
133
+ Bme1580I: GKGCMC 5
134
+ BmtI: GCTAGC 5
135
+ BmyI: GDGCHC 5
136
+ BoxI: GACNNNNGTC 5
137
+ Bpu14I: TTCGAA 2
138
+ Bpu1102I: GCTNAGC 2
139
+ Bsa29I: ATCGAT 2
140
+ BsaAI: YACGTR 3
141
+ BsaBI: GATNNNNATC 5
142
+ BsaHI: GRCGYC 2
143
+ BsaJI: CCNNGG 1
144
+ BsaOI: CGRYCG 4
145
+ BsaWI: WCCGGW 1
146
+ BscI: ATCGAT 2
147
+ Bsc4I: CCNNNNNNNGG 7
148
+ BscBI: GGNNCC 3
149
+ BscFI: GATC 0
150
+ Bse8I: GATNNNNATC 5
151
+ Bse21I: CCTNAGG 2
152
+ Bse118I: RCCGGY 1
153
+ BseAI: TCCGGA 1
154
+ BseBI: CCWGG 2
155
+ BseCI: ATCGAT 2
156
+ BseDI: CCNNGG 1
157
+ BseJI: GATNNNNATC 5
158
+ BseLI: CCNNNNNNNGG 7
159
+ BsePI: GCGCGC 1
160
+ BseSI: GKGCMC 5
161
+ BseX3I: CGGCCG 1
162
+ BshI: GGCC 2
163
+ Bsh1236I: CGCG 2
164
+ Bsh1285I: CGRYCG 4
165
+ BshFI: GGCC 2
166
+ BshNI: GGYRCC 1
167
+ BshTI: ACCGGT 1
168
+ BsiBI: GATNNNNATC 5
169
+ BsiCI: TTCGAA 2
170
+ BsiEI: CGRYCG 4
171
+ BsiHKAI: GWGCWC 5
172
+ BsiHKCI: CYCGRG 1
173
+ BsiLI: CCWGG 2
174
+ BsiMI: TCCGGA 1
175
+ BsiQI: TGATCA 1
176
+ BsiSI: CCGG 1
177
+ BsiWI: CGTACG 1
178
+ BsiXI: ATCGAT 2
179
+ BsiYI: CCNNNNNNNGG 7
180
+ BsiZI: GGNCC 1
181
+ BslI: CCNNNNNNNGG 7
182
+ BsoBI: CYCGRG 1
183
+ Bsp13I: TCCGGA 1
184
+ Bsp19I: CCATGG 1
185
+ Bsp68I: TCGCGA 3
186
+ Bsp106I: ATCGAT 2
187
+ Bsp119I: TTCGAA 2
188
+ Bsp120I: GGGCCC 1
189
+ Bsp143I: GATC 0
190
+ Bsp143II: RGCGCY 5
191
+ Bsp1286I: GDGCHC 5
192
+ Bsp1407I: TGTACA 1
193
+ Bsp1720I: GCTNAGC 2
194
+ BspA2I: CCTAGG 1
195
+ BspCI: CGATCG 4
196
+ BspDI: ATCGAT 2
197
+ BspEI: TCCGGA 1
198
+ BspHI: TCATGA 1
199
+ BspLI: GGNNCC 3
200
+ BspLU11I: ACATGT 1
201
+ BspMII: TCCGGA 1
202
+ BspTI: CTTAAG 1
203
+ BspT104I: TTCGAA 2
204
+ BspT107I: GGYRCC 1
205
+ BspXI: ATCGAT 2
206
+ BsrBRI: GATNNNNATC 5
207
+ BsrFI: RCCGGY 1
208
+ BsrGI: TGTACA 1
209
+ BssAI: RCCGGY 1
210
+ BssECI: CCNNGG 1
211
+ BssHI: CTCGAG 1
212
+ BssHII: GCGCGC 1
213
+ BssKI: CCNGG 0
214
+ BssNAI: GTATAC 3
215
+ BssT1I: CCWWGG 1
216
+ Bst98I: CTTAAG 1
217
+ Bst1107I: GTATAC 3
218
+ BstACI: GRCGYC 2
219
+ BstAPI: GCANNNNNTGC 7
220
+ BstBI: TTCGAA 2
221
+ BstBAI: YACGTR 3
222
+ Bst4CI: ACNGT 3
223
+ BstC8I: GCNNGC 3
224
+ BstDEI: CTNAG 1
225
+ BstDSI: CCRYGG 1
226
+ BstEII: GGTNACC 1
227
+ BstENI: CCTNNNNNAGG 5
228
+ BstENII: GATC 0
229
+ BstFNI: CGCG 2
230
+ BstH2I: RGCGCY 5
231
+ BstHHI: GCGC 3
232
+ BstHPI: GTTAAC 3
233
+ BstKTI: GATC 3
234
+ BstMAI: CTGCAG 5
235
+ BstMCI: CGRYCG 4
236
+ BstMWI: GCNNNNNNNGC 7
237
+ BstNI: CCWGG 2
238
+ BstNSI: RCATGY 5
239
+ BstOI: CCWGG 2
240
+ BstPI: GGTNACC 1
241
+ BstPAI: GACNNNNGTC 5
242
+ BstSCI: CCNGG 0
243
+ BstSFI: CTRYAG 1
244
+ BstSNI: TACGTA 3
245
+ BstUI: CGCG 2
246
+ Bst2UI: CCWGG 2
247
+ BstXI: CCANNNNNNTGG 8
248
+ BstX2I: RGATCY 1
249
+ BstYI: RGATCY 1
250
+ BstZI: CGGCCG 1
251
+ BstZ17I: GTATAC 3
252
+ Bsu15I: ATCGAT 2
253
+ Bsu36I: CCTNAGG 2
254
+ BsuRI: GGCC 2
255
+ BsuTUI: ATCGAT 2
256
+ BtgI: CCRYGG 1
257
+ BthCI: GCNGC 4
258
+
259
+ # =========================================================================== #
260
+ # === c tag
261
+ # =========================================================================== #
262
+ Cac8I: GCNNGC 3
263
+ CaiI: CAGNNNCTG 6
264
+ CauII: CCSGG 2
265
+ CciNI: GCGGCCGC 2
266
+ CelII: GCTNAGC 2
267
+ CfoI: GCGC 3
268
+ CfrI: YGGCCR 1
269
+ Cfr9I: CCCGGG 1
270
+ Cfr10I: RCCGGY 1
271
+ Cfr13I: GGNCC 1
272
+ Cfr42I: CCGCGG 4
273
+ ChaI: GATC 4
274
+ ClaI: ATCGAT 2
275
+ CpoI: CGGWCCG 2
276
+ CspI: CGGWCCG 2
277
+ Csp6I: GTAC 1
278
+ Csp45I: TTCGAA 2
279
+ CspAI: ACCGGT 1
280
+ CviAII: CATG 1
281
+ CviJI: RGCY 2
282
+ CviRI: TGCA 2
283
+ CviTI: RGCY 2
284
+ CvnI: CCTNAGG 2
285
+
286
+ # =========================================================================== #
287
+ # === d tig
288
+ # =========================================================================== #
289
+ DdeI: CTNAG 1
290
+ DpnI: GATC 2
291
+ DpnII: GATC 0
292
+ DraI: TTTAAA 3
293
+ DraII: RGGNCCY 2
294
+ DraIII: CACNNNGTG 6
295
+ DrdI: GACNNNNNNGTC 7
296
+ DsaI: CCRYGG 1
297
+ DseDI: GACNNNNNNGTC 7
298
+
299
+ # =========================================================================== #
300
+ # === e tig
301
+ # =========================================================================== #
302
+ EaeI: YGGCCR 1
303
+ EagI: CGGCCG 1
304
+ Eam1105I: GACNNNNNGTC 6
305
+ Ecl136II: GAGCTC 3
306
+ EclHKI: GACNNNNNGTC 6
307
+ EclXI: CGGCCG 1
308
+ Eco24I: GRGCYC 5
309
+ Eco32I: GATATC 3
310
+ Eco47I: GGWCC 1
311
+ Eco47III: AGCGCT 3
312
+ Eco52I: CGGCCG 1
313
+ Eco72I: CACGTG 3
314
+ Eco81I: CCTNAGG 2
315
+ Eco88I: CYCGRG 1
316
+ Eco91I: GGTNACC 1
317
+ Eco105I: TACGTA 3
318
+ Eco130I: CCWWGG 1
319
+ Eco147I: AGGCCT 3
320
+ EcoHI: CCSGG 0
321
+ EcoICRI: GAGCTC 3
322
+ EcoNI: CCTNNNNNAGG 5
323
+ EcoO65I: GGTNACC 1
324
+ EcoO109I: RGGNCCY 2
325
+ EcoRI: GAATTC 1
326
+ EcoRII: CCWGG 0
327
+ EcoRV: GATATC 3
328
+ EcoT14I: CCWWGG 1
329
+ EcoT22I: ATGCAT 5
330
+ EcoT38I: GRGCYC 5
331
+ EgeI: GGCGCC 3
332
+ EheI: GGCGCC 3
333
+ ErhI: CCWWGG 1
334
+ EsaBC3I: TCGA 2
335
+ EspI: GCTNAGC 2
336
+
337
+ # =========================================================================== #
338
+ # === f tig
339
+ # =========================================================================== #
340
+ FatI: CATG 0
341
+ FauNDI: CATATG 2
342
+ FbaI: TGATCA 1
343
+ FblI: GTMKAC 2
344
+ FmuI: GGNCC 4
345
+ FnuDII: CGCG 2
346
+ Fnu4HI: GCNGC 2
347
+ FriOI: GRGCYC 5
348
+ FseI: GGCCGGCC 6
349
+ FspI: TGCGCA 3
350
+ FspAI: RTGCGCAY 4
351
+ Fsp4HI: GCNGC 2
352
+ FunI: AGCGCT 3
353
+ FunII: GAATTC 1
354
+
355
+ # =========================================================================== #
356
+ # === h tig
357
+ # =========================================================================== #
358
+ HaeI: WGGCCW 3
359
+ HaeII: RGCGCY 5
360
+ HaeIII: GGCC 2
361
+ HapII: CCGG 1
362
+ HgiAI: GWGCWC 5
363
+ HgiCI: GGYRCC 1
364
+ HgiJII: GRGCYC 5
365
+ HhaI: GCGC 3
366
+ Hin1I: GRCGYC 2
367
+ Hin6I: GCGC 1
368
+ HinP1I: GCGC 1
369
+ HincII: GTYRAC 3
370
+ HindII: GTYRAC 3
371
+ HindIII: AAGCTT 1
372
+ HinfI: GANTC 1
373
+ HpaI: GTTAAC 3
374
+ HpaII: CCGG 1
375
+ Hpy8I: GTNNAC 3
376
+ Hpy99I: CGWCG 5
377
+ Hpy178III: TCNNGA 2
378
+ Hpy188I: TCNGA 3
379
+ Hpy188III: TCNNGA 2
380
+ HpyCH4I: CATG 3
381
+ HpyCH4III: ACNGT 3
382
+ HpyCH4IV: ACGT 1
383
+ HpyCH4V: TGCA 2
384
+ HpyF10VI: GCNNNNNNNGC 8
385
+ Hsp92I: GRCGYC 2
386
+ Hsp92II: CATG 4
387
+ HspAI: GCGC 1
388
+ ItaI: GCNGC 2
389
+ KasI: GGCGCC 1
390
+ KpnI: GGTACC 5
391
+ Kpn2I: TCCGGA 1
392
+ KspI: CCGCGG 4
393
+ Ksp22I: TGATCA 1
394
+ KspAI: GTTAAC 3
395
+ Kzo9I: GATC 0
396
+
397
+ # =========================================================================== #
398
+ # === l tig
399
+ # =========================================================================== #
400
+ LpnI: RGCGCY 3
401
+ LspI: TTCGAA 2
402
+
403
+ # =========================================================================== #
404
+ # === m tig
405
+ # =========================================================================== #
406
+ MabI: ACCWGGT 1
407
+ MaeI: CTAG 1
408
+ MaeII: ACGT 1
409
+ MaeIII: GTNAC 0
410
+ MamI: GATNNNNATC 5
411
+ MboI: GATC 0
412
+ McrI: CGRYCG 4
413
+ MfeI: CAATTG 1
414
+ MflI: RGATCY 1
415
+ MhlI: GDGCHC 5
416
+ MlsI: TGGCCA 3
417
+ MluI: ACGCGT 1
418
+ MluNI: TGGCCA 3
419
+ Mly113I: GGCGCC 2
420
+ Mph1103I: ATGCAT 5
421
+ MroI: TCCGGA 1
422
+ MroNI: GCCGGC 1
423
+ MroXI: GAANNNNTTC 5
424
+ MscI: TGGCCA 3
425
+ MseI: TTAA 1
426
+ MslI: CAYNNNNRTG 5
427
+ MspI: CCGG 1
428
+ Msp20I: TGGCCA 3
429
+ MspA1I: CMGCKG 3
430
+ MspCI: CTTAAG 1
431
+ MspR9I: CCNGG 2
432
+ MssI: GTTTAAAC 4
433
+ MstI: TGCGCA 3
434
+ MunI: CAATTG 1
435
+ MvaI: CCWGG 2
436
+ MvnI: CGCG 2 blunt
437
+ MwoI: GCNNNNNNNGC 7
438
+
439
+ # =========================================================================== #
440
+ # === n tig
441
+ # =========================================================================== #
442
+ NciI: CC/SGG 2
443
+ NaeI: GCCGGC 3
444
+ NarI: GGCGCC 2
445
+ NciI: CCSGG 2
446
+ NcoI: CCATGG 1
447
+ NdeI: CATATG 2
448
+ NdeII: GATC 0
449
+ NgoAIV: GCCGGC 1
450
+ NgoMIV: GCCGGC 1
451
+ NheI: GCTAGC 1
452
+ NlaIII: CATG 4
453
+ NlaIV: GGNNCC 3
454
+ Nli3877I: CYCGRG 5
455
+ NmuCI: GTSAC 0
456
+ NotI: GCGGCCGC 2
457
+ NruI: TCGCGA 3
458
+ NruGI: GACNNNNNGTC 6
459
+ NsbI: TGCGCA 3
460
+ NsiI: ATGCAT 5
461
+ NspI: RCATGY 5
462
+ NspIII: CYCGRG 1
463
+ NspV: TTCGAA 2
464
+ NspBII: CMGCKG 3
465
+
466
+ # =========================================================================== #
467
+ # === o tig
468
+ # =========================================================================== #
469
+ OliI: CACNNNNGTG 5
470
+
471
+ # =========================================================================== #
472
+ # === p tig
473
+ # =========================================================================== #
474
+ PacI: TTAATTAA 5
475
+ PaeI: GCATGC 5
476
+ PaeR7I: CTCGAG 1
477
+ PagI: TCATGA 1
478
+ PalI: GGCC 2
479
+ PauI: GCGCGC 1
480
+ PceI: AGGCCT 3
481
+ PciI: ACATGT 1
482
+ PdiI: GCCGGC 3
483
+ PdmI: GAANNNNTTC 5
484
+ Pfl23II: CGTACG 1
485
+ PflBI: CCANNNNNTGG 7
486
+ PflFI: GACNNNGTC 4
487
+ PflMI: CCANNNNNTGG 7
488
+ PfoI: TCCNGGA 1
489
+ PinAI: ACCGGT 1
490
+ Ple19I: CGATCG 4
491
+ PmaCI: CACGTG 3
492
+ PmeI: GTTTAAAC 4
493
+ PmlI: CACGTG 3
494
+ Ppu10I: ATGCAT 1
495
+ PpuMI: RGGWCCY 2
496
+ PpuXI: RGGWCCY 2
497
+ PshAI: GACNNNNGTC 5
498
+ PshBI: ATTAAT 2
499
+ PsiI: TTATAA 3
500
+ Psp03I: GGWCC 4
501
+ Psp5II: RGGWCCY 2
502
+ Psp6I: CCWGG 0
503
+ Psp1406I: AACGTT 2
504
+ PspAI: CCCGGG 1
505
+ Psp124BI: GAGCTC 5
506
+ PspEI: GGTNACC 1
507
+ PspGI: CCWGG 0
508
+ PspLI: CGTACG 1
509
+ PspN4I: GGNNCC 3
510
+ PspOMI: GGGCCC 1
511
+ PspPI: GGNCC 1
512
+ PspPPI: RGGWCCY 2
513
+ PssI: RGGNCCY 5
514
+ PstI: CTGCAG 5
515
+ PsuI: RGATCY 1
516
+ PsyI: GACNNNGTC 4
517
+ PvuI: CGATCG 4
518
+ PvuII: CAGCTG 3
519
+ RcaI: TCATGA 1
520
+ RsaI: GTAC 2
521
+ RsrII: CGGWCCG 2
522
+ Rsr2I: CGGWCCG 2
523
+
524
+ # =========================================================================== #
525
+ # === s tig
526
+ # =========================================================================== #
527
+ SacI: GAGCTC 5
528
+ SacII: CCGCGG 4
529
+ SalI: GTCGAC 1
530
+ SanDI: GGGWCCC 2
531
+ SatI: GCNGC 2
532
+ SauI: CCTNAGG 2
533
+ Sau96I: GGNCC 1
534
+ Sau3AI: GATC 0
535
+ SbfI: CCTGCAGG 6
536
+ ScaI: AGTACT 3
537
+ SciI: CTCGAG 3
538
+ ScrFI: CCNGG 2
539
+ SdaI: CCTGCAGG 6
540
+ SduI: GDGCHC 5
541
+ SecI: CCNNGG 1
542
+ SelI: CGCG 0
543
+ SexAI: ACCWGGT 1
544
+ SfcI: CTRYAG 1
545
+ SfeI: CTRYAG 1
546
+ SfiI: GGCCNNNNNGGCC 8
547
+ SfoI: GGCGCC 3
548
+ Sfr274I: CTCGAG 1
549
+ Sfr303I: CCGCGG 4
550
+ SfuI: TTCGAA 2
551
+ SgfI: GCGATCGC 5
552
+ SgrAI: CRCCGGYG 2
553
+ SgrBI: CCGCGG 4
554
+ SinI: GGWCC 1
555
+ SlaI: CTCGAG 1
556
+ SmaI: CCCGGG 3 # This is a blunt-cutter.
557
+ SmiI: ATTTAAAT 4
558
+ SmiMI: CAYNNNNRTG 5
559
+ SmlI: CTYRAG 1
560
+ SnaBI: TACGTA 3
561
+ SpaHI: GCATGC 5
562
+ SpeI: ACTAGT 1
563
+ SphI: GCATGC 5
564
+ SplI: CGTACG 1
565
+ SrfI: GCCCGGGC 4
566
+ Sse9I: AATT 0
567
+ Sse232I: CGCCGGCG 2
568
+ Sse8387I: CCTGCAGG 6
569
+ Sse8647I: AGGWCCT 2
570
+ SseBI: AGGCCT 3
571
+ SspI: AATATT 3
572
+ SspBI: TGTACA 1
573
+ SstI: GAGCTC 5
574
+ SstII: CCGCGG 4
575
+ StuI: AGGCCT 3
576
+ StyI: CCWWGG 1
577
+ SunI: CGTACG 1
578
+ SwaI: ATTTAAAT 4
579
+
580
+ # =========================================================================== #
581
+ # === t tig
582
+ # =========================================================================== #
583
+ TaaI: ACNGT 3
584
+ TaiI: ACGT 4
585
+ TaqI: TCGA 1
586
+ TasI: AATT 0
587
+ TatI: WGTACW 1
588
+ TauI: GCSGC 4
589
+ TelI: GACNNNGTC 4
590
+ TfiI: GAWTC 1
591
+ ThaI: CGCG 2
592
+ TliI: CTCGAG 1
593
+ Tru1I: TTAA 1
594
+ Tru9I: TTAA 1
595
+ TscI: ACGT 4
596
+ TseI: GCWGC 1
597
+ Tsp45I: GTSAC 0
598
+ Tsp509I: AATT 0
599
+ Tsp4CI: ACNGT 3
600
+ TspEI: AATT 0
601
+ Tth111I: GACNNNGTC 4
602
+ TthHB8I: TCGA 1
603
+ UnbI: GGNCC 0
604
+ Van91I: CCANNNNNTGG 7
605
+ Vha464I: CTTAAG 1
606
+ VneI: GTGCAC 1
607
+ VpaK11AI: GGWCC 0
608
+ VpaK11BI: GGWCC 1
609
+ VspI: ATTAAT 2
610
+ XagI: CCTNNNNNAGG 5
611
+ XapI: RAATTY 1
612
+ XbaI: TCTAGA 1
613
+ XceI: RCATGY 5
614
+ XcmI: CCANNNNNNNNNTGG 8
615
+ XhoI: CTCGAG 1
616
+ XhoII: RGATCY 1
617
+ XmaI: CCCGGG 1
618
+ XmaIII: CGGCCG 1
619
+ XmaCI: CCCGGG 1
620
+ XmaJI: CCTAGG 1
621
+ XmiI: GTMKAC 2
622
+ XmnI: GAANNNNTTC 5
623
+ XspI: CTAG 1
624
+
625
+ # =========================================================================== #
626
+ # === z tig
627
+ # =========================================================================== #
628
+ ZhoI: ATCGAT 2
629
+ ZraI: GACGTC 3
630
+ Zsp2I: ATGCAT 5
data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta ADDED
@@ -0,0 +1,14 @@
1
+ >ENA|JX472995|JX472995.1 Aequorea victoria isolate sGFP-206 green fluorescent protein (gfp) gene, partial cds. URL: https://www.ebi.ac.uk/ena/data/view/JX472995
2
+ ATGCGTAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGT
3
+ GATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACAAACGGA
4
+ AAACTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTT
5
+ GTCACTACTTTGACTTATGGTGTTCAATGCTTTGCGAGATACCCAGATCATATGAAACAG
6
+ CATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAAAGAACTATATCTTTC
7
+ AAAGATGACGGGACCTACAAGACACGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTT
8
+ AATAGAATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAA
9
+ TTGGAATACAACTTTAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGA
10
+ ATCAAAGCTAACTTCAAAATTAGACACAACGTTGAAGATGGAAGCGTTCAACTAGCAGAC
11
+ CATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTAC
12
+ CTGTCCACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCACATGGTCCTT
13
+ CTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGGATGAACTATACAAAAGGCCT
14
+ GCAGCAAACGACGAAAACTACGCTGCATCAGTT
data/lib/bioroebe/yaml/sequences/README.md ADDED
@@ -0,0 +1,2 @@
1
+ This directory may contain individual FASTA entries, which can be used
2
+ for testing-purposes and similar.
data/lib/bioroebe/yaml/talens.yml ADDED
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+ # =========================================================================== #
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+ # === talens.yml
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+ #
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+ # This file will contain the aminoacids at which sites TALENs will then cut.
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+ #
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+ # It has been obtained from the following paper:
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+ #
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+ # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130291/figure/F1/
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+ #
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+ # =========================================================================== #
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+
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+ A:
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+ NI # Asparagine, Isoleucin
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+
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+ T:
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+ NG # Asparagine, Glycine
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+
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+ C:
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+ HD # Histidin, Aspartate
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+
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+ G:
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+ NN # Asparagine, Asparagine