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
  619. data/lib/bioroebe/toplevel_methods/infer.rb +66 -0
  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
  623. data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
  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
  630. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
  631. data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
  632. data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
  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
  732. data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
  733. data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
  734. data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
  735. data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
  736. data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
  737. data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
  738. data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
  739. data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
  740. data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
  741. data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
  742. data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
  743. data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
  744. data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
  745. data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
  746. data/lib/bioroebe/yaml/configuration/README.md +12 -0
  747. data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
  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
  763. data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
  764. data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
  765. data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
  766. data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
  767. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
  768. data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
  769. data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
  770. data/lib/bioroebe/yaml/pathways/README.md +2 -0
  771. data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
  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
  781. data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
  782. data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
  783. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
  784. data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
  785. data/lib/bioroebe/yaml/sequences/README.md +2 -0
  786. data/lib/bioroebe/yaml/talens.yml +22 -0
  787. data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
  788. data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
  789. data/lib/bioroebe.rb +5 -0
  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/base_composition_of_dna.yml ADDED
@@ -0,0 +1,37 @@
1
+ # =========================================================================== #
2
+ # === base_composition_of_dna.yml
3
+ #
4
+ # The dataset came from the book "Genetics", from 2014.
5
+ #
6
+ # x = YAML.load_file('base_composition_of_dna.yml')
7
+ # =========================================================================== #
8
+
9
+ Escherichia_coli:
10
+ A: 26.0
11
+ T: 23.9
12
+ G: 24.9
13
+ C: 25.2
14
+
15
+ Yeast:
16
+ A: 31.3
17
+ T: 32.9
18
+ G: 18.7
19
+ C: 17.1
20
+
21
+ Sea_urchin:
22
+ A: 32.8
23
+ T: 32.1
24
+ G: 17.7
25
+ C: 18.4
26
+
27
+ Rat:
28
+ A: 28.6
29
+ T: 28.4
30
+ G: 21.4
31
+ C: 21.5
32
+
33
+ Human:
34
+ A: 30.3
35
+ T: 30.3
36
+ G: 19.5
37
+ C: 19.9
data/lib/bioroebe/yaml/blosum/blosum45.yml ADDED
@@ -0,0 +1,36 @@
1
+ # =========================================================================== #
2
+ # === blosum45.yml
3
+ #
4
+ # Entries for the BLOSUM45 matrix at a scale of ln(2)/3.0
5
+ #
6
+ # A reference implementation can be seen here:
7
+ #
8
+ # https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM45
9
+ #
10
+ # =========================================================================== #
11
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
12
+ A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 -1 -1 -5
13
+ R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 -3 1 -1 -5
14
+ N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 5 -3 0 -1 -5
15
+ D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 6 -3 1 -1 -5
16
+ C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -2 -3 -1 -5
17
+ Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 -2 4 -1 -5
18
+ E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 -3 5 -1 -5
19
+ G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -4 -2 -1 -5
20
+ H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 -2 0 -1 -5
21
+ I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 4 -3 -1 -5
22
+ L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 4 -2 -1 -5
23
+ K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 -3 1 -1 -5
24
+ M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 2 -1 -1 -5
25
+ F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 1 -3 -1 -5
26
+ P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -3 -1 -1 -5
27
+ S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 -2 0 -1 -5
28
+ T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 -1 -1 -5
29
+ W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -1 -5
30
+ Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 0 -2 -1 -5
31
+ V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 2 -3 -1 -5
32
+ B -1 -1 5 6 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 5 -3 1 -1 -5
33
+ J -1 -3 -3 -3 -2 -2 -3 -4 -2 4 4 -3 2 1 -3 -2 -1 -2 0 2 -3 4 -2 -1 -5
34
+ Z -1 1 0 1 -3 4 5 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 1 -2 5 -1 -5
35
+ X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -5
36
+ * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
data/lib/bioroebe/yaml/blosum/blosum50.yml ADDED
@@ -0,0 +1,34 @@
1
+ # === blosum50.yml
2
+ #
3
+ # A reference implementation can be seen here:
4
+ #
5
+ # https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM50
6
+ #
7
+ # =========================================================================== #
8
+
9
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
10
+ A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -2 -1 -1 -5
11
+ R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 -3 0 -1 -5
12
+ N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 5 -4 0 -1 -5
13
+ D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 6 -4 1 -1 -5
14
+ C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -2 -3 -1 -5
15
+ Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 -3 4 -1 -5
16
+ E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 -3 5 -1 -5
17
+ G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -4 -2 -1 -5
18
+ H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 -3 0 -1 -5
19
+ I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 4 -3 -1 -5
20
+ L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 4 -3 -1 -5
21
+ K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 -3 1 -1 -5
22
+ M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 2 -1 -1 -5
23
+ F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 1 -4 -1 -5
24
+ P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -3 -1 -1 -5
25
+ S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 -3 0 -1 -5
26
+ T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 -1 -1 -5
27
+ W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -2 -1 -5
28
+ Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -1 -2 -1 -5
29
+ V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -3 2 -3 -1 -5
30
+ B -2 -1 5 6 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -3 6 -4 1 -1 -5
31
+ J -2 -3 -4 -4 -2 -3 -3 -4 -3 4 4 -3 2 1 -3 -3 -1 -2 -1 2 -4 4 -3 -1 -5
32
+ Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 1 -3 5 -1 -5
33
+ X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -5
34
+ * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
data/lib/bioroebe/yaml/blosum/blosum62.yml ADDED
@@ -0,0 +1,35 @@
1
+ # =========================================================================== #
2
+ # === blosum62.yml
3
+ #
4
+ # A reference implementation can be seen here:
5
+ #
6
+ # https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
7
+ #
8
+ # =========================================================================== #
9
+
10
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
11
+ A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -1 -4
12
+ R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 -2 0 -1 -4
13
+ N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 -3 0 -1 -4
14
+ D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 -3 1 -1 -4
15
+ C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -1 -3 -1 -4
16
+ Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 -2 4 -1 -4
17
+ E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 -3 4 -1 -4
18
+ G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -4 -2 -1 -4
19
+ H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 -3 0 -1 -4
20
+ I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 3 -3 -1 -4
21
+ L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 3 -3 -1 -4
22
+ K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 -3 1 -1 -4
23
+ M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 2 -1 -1 -4
24
+ F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 0 -3 -1 -4
25
+ P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -3 -1 -1 -4
26
+ S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 -2 0 -1 -4
27
+ T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 -1 -1 -4
28
+ W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -2 -2 -1 -4
29
+ Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -1 -2 -1 -4
30
+ V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 2 -2 -1 -4
31
+ B -2 -1 4 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 -3 0 -1 -4
32
+ J -1 -2 -3 -3 -1 -2 -3 -4 -3 3 3 -3 2 0 -3 -2 -1 -2 -1 2 -3 3 -3 -1 -4
33
+ Z -1 0 0 1 -3 4 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -2 -2 -2 0 -3 4 -1 -4
34
+ X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4
35
+ * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
data/lib/bioroebe/yaml/blosum/blosum80.yml ADDED
@@ -0,0 +1,37 @@
1
+ # =========================================================================== #
2
+ # === blosum80.yml
3
+ #
4
+ # Entries for the BLOSUM80 matrix at a scale of ln(2)/2.0
5
+ #
6
+ # A reference implementation can be seen here:
7
+ #
8
+ # https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM80
9
+ #
10
+ # =========================================================================== #
11
+
12
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
13
+ A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -2 -1 -1 -6
14
+ R -2 6 -1 -2 -4 1 -1 -3 0 -3 -3 2 -2 -4 -2 -1 -1 -4 -3 -3 -1 -3 0 -1 -6
15
+ N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -4 5 -4 0 -1 -6
16
+ D -2 -2 1 6 -4 -1 1 -2 -2 -4 -5 -1 -4 -4 -2 -1 -1 -6 -4 -4 5 -5 1 -1 -6
17
+ C -1 -4 -3 -4 9 -4 -5 -4 -4 -2 -2 -4 -2 -3 -4 -2 -1 -3 -3 -1 -4 -2 -4 -1 -6
18
+ Q -1 1 0 -1 -4 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -3 -2 -3 0 -3 4 -1 -6
19
+ E -1 -1 -1 1 -5 2 6 -3 0 -4 -4 1 -2 -4 -2 0 -1 -4 -3 -3 1 -4 5 -1 -6
20
+ G 0 -3 -1 -2 -4 -2 -3 6 -3 -5 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4 -1 -5 -3 -1 -6
21
+ H -2 0 0 -2 -4 1 0 -3 8 -4 -3 -1 -2 -2 -3 -1 -2 -3 2 -4 -1 -4 0 -1 -6
22
+ I -2 -3 -4 -4 -2 -3 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -4 3 -4 -1 -6
23
+ L -2 -3 -4 -5 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -2 1 -4 3 -3 -1 -6
24
+ K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 -1 -1 -4 -3 -3 -1 -3 1 -1 -6
25
+ M -1 -2 -3 -4 -2 0 -2 -4 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 2 -1 -1 -6
26
+ F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 0 6 -4 -3 -2 0 3 -1 -4 0 -4 -1 -6
27
+ P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -3 -1 -3 -4 8 -1 -2 -5 -4 -3 -2 -4 -2 -1 -6
28
+ S 1 -1 0 -1 -2 0 0 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -3 0 -1 -6
29
+ T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -2 1 5 -4 -2 0 -1 -1 -1 -1 -6
30
+ W -3 -4 -4 -6 -3 -3 -4 -4 -3 -3 -2 -4 -2 0 -5 -4 -4 11 2 -3 -5 -3 -3 -1 -6
31
+ Y -2 -3 -3 -4 -3 -2 -3 -4 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -3 -2 -3 -1 -6
32
+ V 0 -3 -4 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 2 -3 -1 -6
33
+ B -2 -1 5 5 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 5 -4 0 -1 -6
34
+ J -2 -3 -4 -5 -2 -3 -4 -5 -4 3 3 -3 2 0 -4 -3 -1 -3 -2 2 -4 3 -3 -1 -6
35
+ Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -1 -4 -2 0 -1 -3 -3 -3 0 -3 5 -1 -6
36
+ X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
37
+ * -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
data/lib/bioroebe/yaml/blosum/blosum90.yml ADDED
@@ -0,0 +1,36 @@
1
+ # =========================================================================== #
2
+ # === blosum90.yml
3
+ #
4
+ # Entries for the BLOSUM90 matrix at a scale of ln(2)/2.0
5
+ #
6
+ # A reference implementation can be seen here:
7
+ #
8
+ # https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM90
9
+ #
10
+ # =========================================================================== #
11
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
12
+ A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -2 -1 -1 -6
13
+ R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 -3 0 -1 -6
14
+ N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 5 -4 -1 -1 -6
15
+ D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 5 -5 1 -1 -6
16
+ C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -2 -5 -1 -6
17
+ Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 -3 5 -1 -6
18
+ E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 1 -4 5 -1 -6
19
+ G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -5 -3 -1 -6
20
+ H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 -4 0 -1 -6
21
+ I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 3 -4 -1 -6
22
+ L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 4 -4 -1 -6
23
+ K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 -3 1 -1 -6
24
+ M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 2 -2 -1 -6
25
+ F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 0 -4 -1 -6
26
+ P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -4 -2 -1 -6
27
+ S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -3 -1 -1 -6
28
+ T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -2 -1 -1 -6
29
+ W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -3 -4 -1 -6
30
+ Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -2 -3 -1 -6
31
+ V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 1 -3 -1 -6
32
+ B -2 -2 5 5 -4 -1 1 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 5 -5 0 -1 -6
33
+ J -2 -3 -4 -5 -2 -3 -4 -5 -4 3 4 -3 2 0 -4 -3 -2 -3 -2 1 -5 4 -4 -1 -6
34
+ Z -1 0 -1 1 -5 5 5 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 -4 5 -1 -6
35
+ X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
36
+ * -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
data/lib/bioroebe/yaml/blosum/blosum_matrix.yml ADDED
@@ -0,0 +1,200 @@
1
+ # =========================================================================== #
2
+ # === blosum_matrix.yml
3
+ #
4
+ # This file has 8 rows. It is a test matrix - should allow you to
5
+ # test out things more easily than the other blosum-yaml files.
6
+ # =========================================================================== #
7
+ # y = YAML.load_file('blosum_matrix.yml')
8
+ # =========================================================================== #
9
+
10
+ # =========================================================================== #
11
+ # Aminoacid A, Alanin.
12
+ # =========================================================================== #
13
+ AA: 5
14
+ AC: -1
15
+ AD: -2
16
+ AE: -1
17
+ AF: -2
18
+ AG: 0
19
+ AH: -2
20
+ AI: -1
21
+ AK: -1
22
+ AL: -1
23
+ AM: -1
24
+ AN: -1
25
+ AP: -1
26
+ AQ: -1
27
+ AR: -2
28
+ AS: 1
29
+ AT: 0
30
+ AV: 0
31
+ AW: -2
32
+ AY: -2
33
+
34
+ # =========================================================================== #
35
+ # Aminoacid C, Cystein
36
+ # =========================================================================== #
37
+ CA: -1
38
+ CC: 12
39
+ CD: -3
40
+ CE: -3
41
+ CF: -2
42
+ CG: -3
43
+ CH: -3
44
+ CI: -3
45
+ CK: -3
46
+ CL: -2
47
+ CM: -2
48
+ CN: -2
49
+ CP: -4
50
+ CQ: -3
51
+ CR: -3
52
+ CS: -1
53
+ CT: -1
54
+ CV: -1
55
+ CW: -5
56
+ CY: -3
57
+
58
+ # =========================================================================== #
59
+ # Aminoacid D, Aspartic acid.
60
+ # =========================================================================== #
61
+ DA: -2
62
+ DC: -3
63
+ DD: 7
64
+ DE: 2
65
+ DF: -4
66
+ DG: -1
67
+ DH: 0
68
+ DI: -4
69
+ DK: 0
70
+ DL: -3
71
+ DM: -3
72
+ DN: 2
73
+ DP: -1
74
+ DQ: 0
75
+ DR: -1
76
+ DS: 0
77
+ DT: -1
78
+ DV: -3
79
+ DW: -4
80
+ DY: -2
81
+
82
+ # =========================================================================== #
83
+ # Aminoacid E, Glutamat
84
+ # =========================================================================== #
85
+ EA: -1
86
+ EC: -3
87
+ ED: 2
88
+ EE: 6
89
+ EF: -3
90
+ EG: -2
91
+ EH: 0
92
+ EI: -3
93
+ EK: 1
94
+ EL: -2
95
+ EM: -2
96
+ EN: 0
97
+ EP: 0
98
+ EQ: 2
99
+ ER: 0
100
+ ES: 0
101
+ ET: -1
102
+ EV: -3
103
+ EW: -3
104
+ EY: -2
105
+
106
+ # =========================================================================== #
107
+ # Aminoacid G, Glycin
108
+ # =========================================================================== #
109
+ GA: 0
110
+ GC: -3
111
+ GD: -1
112
+ GE: -2
113
+ GF: -3
114
+ GG: 7
115
+ GH: -2
116
+ GI: -4
117
+ GK: -2
118
+ GL: -3
119
+ GM: -2
120
+ GN: 0
121
+ GP: -2
122
+ GQ: -2
123
+ GR: -2
124
+ GS: 0
125
+ GT: -2
126
+ GV: -2
127
+ GW: -2
128
+ GY: -3
129
+
130
+ # =========================================================================== #
131
+ # Aminoacid H, Histidin
132
+ # =========================================================================== #
133
+ HA: -2
134
+ HC: -3
135
+ HD: 0
136
+ HE: 0
137
+ HF: -2
138
+ HG: -2
139
+ HH: 10
140
+ HI: -3
141
+ HK: -1
142
+ HL: -2
143
+ HM: 0
144
+ HN: 1
145
+ HP: -2
146
+ HQ: 1
147
+ HR: 0
148
+ HS: -1
149
+ HT: -2
150
+ HV: -3
151
+ HW: -3
152
+ HY: 2
153
+
154
+ # =========================================================================== #
155
+ # Aminoacid I, Isoleucin
156
+ # =========================================================================== #
157
+ IA: -1
158
+ IC: -3
159
+ ID: -4
160
+ IE: -3
161
+ IF: 0
162
+ IG: -4
163
+ IH: -3
164
+ II: 5
165
+ IK: -3
166
+ IL: 2
167
+ IM: 2
168
+ IN: -2
169
+ IP: -2
170
+ IQ: -2
171
+ IR: -3
172
+ IS: -2
173
+ IT: -1
174
+ IV: 3
175
+ IW: -2
176
+ IY: 0
177
+
178
+ # =========================================================================== #
179
+ # Aminoacid K, Lysin
180
+ # =========================================================================== #
181
+ KA: -1
182
+ KC: -3
183
+ KD: 0
184
+ KE: 1
185
+ KF: -3
186
+ KG: -2
187
+ KH: -1
188
+ KI: -3
189
+ KK: 5
190
+ KL: -3
191
+ KM: -1
192
+ KN: 0
193
+ KP: -1
194
+ KQ: 1
195
+ KR: 3
196
+ KS: -1
197
+ KT: -1
198
+ KV: -2
199
+ KW: -2
200
+ KY: -1
data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml ADDED
@@ -0,0 +1,30 @@
1
+ # =========================================================================== #
2
+ # === chromosome_numbers.yml
3
+ #
4
+ # https://en.wikipedia.org/wiki/List_of_organisms_by_chromosome_count
5
+ # =========================================================================== #
6
+
7
+ # =========================================================================== #
8
+ # Species: 2n
9
+ # =========================================================================== #
10
+ Yellow fever mosquito 6
11
+ Fruit fly: 8
12
+ Yellow Dung Fly: 12
13
+ Guinea Pig: 16
14
+ Snail: 24
15
+ Tibetan fox: 36
16
+ Cat: 38
17
+ Pig: 38
18
+ Mouse: 40
19
+ Syrian hamster: 44
20
+ Hare: 46
21
+ Human: 46
22
+ Ape: 48
23
+ Sheep: 54
24
+ Elephant: 56
25
+ Cow: 60
26
+ Donkey: 62
27
+ Dog: 78
28
+ Chicken: 78
29
+ Carp: 104
30
+ Butterflies: 380
data/lib/bioroebe/yaml/codon_tables/1.yml ADDED
@@ -0,0 +1,113 @@
1
+ # =========================================================================== #
2
+ # === codon table 1, for eukaryotes.
3
+ #
4
+ # This is essentially the most important codon table, number 1, which is
5
+ # valid for (most) eukaryotes.
6
+ #
7
+ # The dataset that this file holds will be stored it in DNA form, just
8
+ # as in its original variant at:
9
+ #
10
+ # https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
11
+ #
12
+ # In rare cases, translation in eukaryotes can be initiated from codons
13
+ # other than AUG. A well documented case (including direct protein
14
+ # sequencing) is the GUG start of a "ribosomal P protein" of the fungus.
15
+ #
16
+ # All the codons must be stored in DNA format.
17
+ #
18
+ # This codon table makes use of three stop codons (in RNA these are
19
+ # UAA, UGA and UAG).
20
+ #
21
+ # =========================================================================== #
22
+ # dataset = YAML.load_file("#{Bioroebe::PROJECT_YAML_DIRECTORY}/codon_tables/1.yml")
23
+ # "#{PROJECT_YAML_DIRECTORY}/codon_tables/1.yml"
24
+ # =========================================================================== #
25
+
26
+ # =========================================================================== #
27
+ # === The Stop Codons
28
+ # =========================================================================== #
29
+ TAA: '*' # Stop Codon.
30
+ TGA: '*' # Stop Codon.
31
+ TAG: '*' # Stop Codon.
32
+
33
+ # =========================================================================== #
34
+ # === The Start Codon
35
+ # =========================================================================== #
36
+ START: ATG # This is the main one in Eukaryotes.
37
+
38
+ # =========================================================================== #
39
+ # === Codons starting with T
40
+ # =========================================================================== #
41
+ TTT: F # Phenylalanine.
42
+ TCT: S # Serine.
43
+ TAT: Y # Tyrosine.
44
+ TGT: C # Cysteine.
45
+ TTC: F # Phenylalanine.
46
+ TCC: S # Serine.
47
+ TAC: Y # Tyrosine.
48
+ TGC: C # Cysteine.
49
+ TTA: L # Leucine.
50
+ TCA: S # Serine.
51
+ TTG: L # Leucine.
52
+ TCG: S # Serine.
53
+ TGG: W # Tryptophane.
54
+
55
+ # =========================================================================== #
56
+ # === Codons starting with C
57
+ # =========================================================================== #
58
+ CTT: L # Leucine.
59
+ CCT: P # Proline.
60
+ CAT: H # Histidine.
61
+ CGT: R # Arginine.
62
+ CTC: L # Leucine.
63
+ CCC: P # Proline.
64
+ CAC: H # Histidine.
65
+ CGC: R # Arginine.
66
+ CTA: L # Leucine.
67
+ CCA: P # Proline.
68
+ CAA: Q # Glutamine.
69
+ CGA: R # Arginine.
70
+ CTG: L # Leucine.
71
+ CCG: P # Proline.
72
+ CAG: Q # Glutamine.
73
+ CGG: R # Arginine.
74
+
75
+ # =========================================================================== #
76
+ # === Codons starting with A
77
+ # =========================================================================== #
78
+ AAG: K # Lysine.
79
+ AAA: K # Lysine.
80
+ ATT: I # Isoleucin.
81
+ ACT: T # Threonine.
82
+ AAT: N # Asparagin.
83
+ AGT: S # Serine.
84
+ ATC: I # Isoleucin.
85
+ ACC: T # Threonine.
86
+ AAC: N # Asparagin.
87
+ AGC: S # Serine.
88
+ ATA: I # Isoleucin.
89
+ ACA: T # Threonine.
90
+ AGA: R # Arginine.
91
+ ATG: M # Methionin. This is also the start-codon.
92
+ ACG: T # Threonine.
93
+ AGG: R # Arginine.
94
+
95
+ # =========================================================================== #
96
+ # === Codons starting with G
97
+ # =========================================================================== #
98
+ GTT: V # Valine.
99
+ GCT: A # Alanine.
100
+ GAT: D # Aspartic Acid.
101
+ GGT: G # Glycine.
102
+ GTC: V # Valine.
103
+ GCC: A # Alanine.
104
+ GAC: D # Aspartic Acid.
105
+ GGC: G # Glycine.
106
+ GTA: V # Valine.
107
+ GCA: A # Alanine.
108
+ GAA: E # Glutamic Acid.
109
+ GGA: G # Glycine.
110
+ GTG: V # Valine.
111
+ GCG: A # Alanine.
112
+ GAG: E # Glutamic Acid.
113
+ GGG: G # Glycine.
data/lib/bioroebe/yaml/codon_tables/10.yml ADDED
@@ -0,0 +1,89 @@
1
+ # =========================================================================== #
2
+ # === 10: Euplotid Nuclear
3
+ #
4
+ # Codon Table 10.
5
+ # =========================================================================== #
6
+
7
+ # =========================================================================== #
8
+ # === Stop Codons
9
+ # =========================================================================== #
10
+ TAG: '*'
11
+ TAA: '*'
12
+
13
+ # =========================================================================== #
14
+ # === Starting with T
15
+ # =========================================================================== #
16
+ TTT: F
17
+ TCT: S
18
+ TAT: Y
19
+ TGT: C
20
+ TTC: F
21
+ TCC: S
22
+ TAC: Y
23
+ TGC: C
24
+ TTA: L
25
+ TCA: S
26
+ TGA: C
27
+ TTG: L
28
+ TCG: S
29
+ TGG: W
30
+
31
+ # =========================================================================== #
32
+ # === Starting with C
33
+ # =========================================================================== #
34
+ CTT: L
35
+ CCT: P
36
+ CAT: H
37
+ CGT: R
38
+ CTC: L
39
+ CCC: P
40
+ CAC: H
41
+ CGC: R
42
+ CTA: L
43
+ CCA: P
44
+ CAA: Q
45
+ CGA: R
46
+ CTG: L
47
+ CCG: P
48
+ CAG: Q
49
+ CGG: R
50
+
51
+ # =========================================================================== #
52
+ # === Starting with A
53
+ # =========================================================================== #
54
+ ATT: I
55
+ ACT: T
56
+ AAT: N
57
+ AGT: S
58
+ ATC: I
59
+ ACC: T
60
+ AAC: N
61
+ AGC: S
62
+ ATA: I
63
+ ACA: T
64
+ AAA: K
65
+ AGA: R
66
+ ATG: M
67
+ ACG: T
68
+ AAG: K
69
+ AGG: R
70
+
71
+ # =========================================================================== #
72
+ # === Starting with G
73
+ # =========================================================================== #
74
+ GTT: V
75
+ GCT: A
76
+ GAT: D
77
+ GGT: G
78
+ GTC: V
79
+ GCC: A
80
+ GAC: D
81
+ GGC: G
82
+ GTA: V
83
+ GCA: A
84
+ GAA: E
85
+ GGA: G
86
+ GTG: V
87
+ GCG: A
88
+ GAG: E
89
+ GGG: G