neurohmmer 0.1.0

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Files changed (133) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +35 -0
  3. data/CODE_OF_CONDUCT.md +13 -0
  4. data/Gemfile +4 -0
  5. data/LICENSE +662 -0
  6. data/README.md +136 -0
  7. data/Rakefile +17 -0
  8. data/bin/neurohmmer +69 -0
  9. data/data/hmm/CRH_DH44.fa.hmm +427 -0
  10. data/data/hmm/Chordate_Glucagon_PACAP.fa.hmm +484 -0
  11. data/data/hmm/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa.hmm +526 -0
  12. data/data/hmm/Deutrostomian_tachykinin.fa.hmm +367 -0
  13. data/data/hmm/Gastrin_releasing_peptide.fa.hmm +448 -0
  14. data/data/hmm/GnRH.fa.hmm +370 -0
  15. data/data/hmm/Hypocretin_orexin.fa.hmm +451 -0
  16. data/data/hmm/Lophotrochozoan_luqin_arthropod_RYamide.fa.hmm +385 -0
  17. data/data/hmm/NPFF.fa.hmm +430 -0
  18. data/data/hmm/NPS.fa.hmm +790 -0
  19. data/data/hmm/PTH.fa.hmm +502 -0
  20. data/data/hmm/Protostomian_Allatostatin_B.fa.hmm +835 -0
  21. data/data/hmm/Protostomian_CCH_amide.fa.hmm +415 -0
  22. data/data/hmm/Protostomian_Ecdysis_Triggering_Hormone.fa.hmm +433 -0
  23. data/data/hmm/Protostomian_PDF.fa.hmm +265 -0
  24. data/data/hmm/Protostomian_allatostatin_C.fa.hmm +352 -0
  25. data/data/hmm/Protostomian_proctolin.fa.hmm +346 -0
  26. data/data/hmm/Putative_chordate_Opioid.fa.hmm +802 -0
  27. data/data/hmm/SIF.fa.hmm +286 -0
  28. data/data/hmm/TRH.fa.hmm +910 -0
  29. data/data/hmm/allatotropin.fa.hmm +433 -0
  30. data/data/hmm/ambulacrarian_amphioxus_NPS-like.fa.hmm +847 -0
  31. data/data/hmm/avp.fa.hmm +475 -0
  32. data/data/hmm/calcitonin_DH31.fa.hmm +418 -0
  33. data/data/hmm/cholecystokinin_sulfakinin.fa.hmm +433 -0
  34. data/data/hmm/chordate_OX26_QRFP.fa.hmm +475 -0
  35. data/data/hmm/chordate_somatostatin_cortistatin_like.fa.hmm +361 -0
  36. data/data/hmm/f_type_SALMF.fa.hmm +811 -0
  37. data/data/hmm/galanin.fa.hmm +391 -0
  38. data/data/hmm/l_type_SALMF.fa.hmm +523 -0
  39. data/data/hmm/nmu_pyrokinin.fa.hmm +424 -0
  40. data/data/hmm/npy_npf.fa.hmm +301 -0
  41. data/data/hmm/protostomian_CCAP.fa.hmm +415 -0
  42. data/data/hmm/protostomian_allatostatinA_buccalin.fa.hmm +706 -0
  43. data/data/hmm/protostomian_leucokinin.fa.hmm +511 -0
  44. data/data/hmm/protostomian_tackykinin.fa.hmm +760 -0
  45. data/data/hmm/tachykinin.fa.hmm +541 -0
  46. data/data/hmm/vertebrate_ghrelin_motilin.fa.hmm +382 -0
  47. data/data/raw_data/CRH_DH44.fa +44 -0
  48. data/data/raw_data/CRH_DH44.fa.aligned.fa +242 -0
  49. data/data/raw_data/Chordate_Glucagon_PACAP.fa +18 -0
  50. data/data/raw_data/Chordate_Glucagon_PACAP.fa.aligned.fa +72 -0
  51. data/data/raw_data/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa +10 -0
  52. data/data/raw_data/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa.aligned.fa +25 -0
  53. data/data/raw_data/Deutrostomian_tachykinin.fa +1283 -0
  54. data/data/raw_data/Deutrostomian_tachykinin.fa.aligned.fa +5707 -0
  55. data/data/raw_data/Gastrin_releasing_peptide.fa +12 -0
  56. data/data/raw_data/Gastrin_releasing_peptide.fa.aligned.fa +25 -0
  57. data/data/raw_data/GnRH.fa +22 -0
  58. data/data/raw_data/GnRH.fa.aligned.fa +66 -0
  59. data/data/raw_data/Hypocretin_orexin.fa +14 -0
  60. data/data/raw_data/Hypocretin_orexin.fa.aligned.fa +49 -0
  61. data/data/raw_data/Lophotrochozoan_luqin_arthropod_RYamide.fa +26 -0
  62. data/data/raw_data/Lophotrochozoan_luqin_arthropod_RYamide.fa.aligned.fa +91 -0
  63. data/data/raw_data/NPFF.fa +16 -0
  64. data/data/raw_data/NPFF.fa.aligned.fa +48 -0
  65. data/data/raw_data/NPS.fa +8 -0
  66. data/data/raw_data/NPS.fa.aligned.fa +24 -0
  67. data/data/raw_data/PTH.fa +24 -0
  68. data/data/raw_data/PTH.fa.aligned.fa +144 -0
  69. data/data/raw_data/Protostomian_Allatostatin_B.fa +17 -0
  70. data/data/raw_data/Protostomian_Allatostatin_B.fa.aligned.fa +120 -0
  71. data/data/raw_data/Protostomian_CCH_amide.fa +24 -0
  72. data/data/raw_data/Protostomian_CCH_amide.fa.aligned.fa +72 -0
  73. data/data/raw_data/Protostomian_Ecdysis_Triggering_Hormone.fa +24 -0
  74. data/data/raw_data/Protostomian_Ecdysis_Triggering_Hormone.fa.aligned.fa +84 -0
  75. data/data/raw_data/Protostomian_PDF.fa +16 -0
  76. data/data/raw_data/Protostomian_PDF.fa.aligned.fa +32 -0
  77. data/data/raw_data/Protostomian_allatostatin_C.fa +28 -0
  78. data/data/raw_data/Protostomian_allatostatin_C.fa.aligned.fa +56 -0
  79. data/data/raw_data/Protostomian_proctolin.fa +16 -0
  80. data/data/raw_data/Protostomian_proctolin.fa.aligned.fa +32 -0
  81. data/data/raw_data/Putative_chordate_Opioid.fa +8 -0
  82. data/data/raw_data/Putative_chordate_Opioid.fa.aligned.fa +32 -0
  83. data/data/raw_data/SIF.fa +28 -0
  84. data/data/raw_data/SIF.fa.aligned.fa +70 -0
  85. data/data/raw_data/TRH.fa +10 -0
  86. data/data/raw_data/TRH.fa.aligned.fa +50 -0
  87. data/data/raw_data/allatotropin.fa +31 -0
  88. data/data/raw_data/allatotropin.fa.aligned.fa +90 -0
  89. data/data/raw_data/ambulacrarian_amphioxus_NPS-like.fa +8 -0
  90. data/data/raw_data/ambulacrarian_amphioxus_NPS-like.fa.aligned.fa +24 -0
  91. data/data/raw_data/avp.fa +28 -0
  92. data/data/raw_data/avp.fa.aligned.fa +70 -0
  93. data/data/raw_data/calcitonin_DH31.fa +36 -0
  94. data/data/raw_data/calcitonin_DH31.fa.aligned.fa +126 -0
  95. data/data/raw_data/cholecystokinin_sulfakinin.fa +28 -0
  96. data/data/raw_data/cholecystokinin_sulfakinin.fa.aligned.fa +84 -0
  97. data/data/raw_data/chordate_OX26_QRFP.fa +10 -0
  98. data/data/raw_data/chordate_OX26_QRFP.fa.aligned.fa +25 -0
  99. data/data/raw_data/chordate_somatostatin_cortistatin_like.fa +10 -0
  100. data/data/raw_data/chordate_somatostatin_cortistatin_like.fa.aligned.fa +20 -0
  101. data/data/raw_data/f_type_SALMF.fa +118 -0
  102. data/data/raw_data/f_type_SALMF.fa.aligned.fa +590 -0
  103. data/data/raw_data/galanin.fa +93 -0
  104. data/data/raw_data/galanin.fa.aligned.fa +552 -0
  105. data/data/raw_data/kisspeptin.fa +16 -0
  106. data/data/raw_data/kisspeptin.fa.aligned.fa +0 -0
  107. data/data/raw_data/l_type_SALMF.fa +68 -0
  108. data/data/raw_data/l_type_SALMF.fa.aligned.fa +170 -0
  109. data/data/raw_data/nmu_pyrokinin.fa +18 -0
  110. data/data/raw_data/nmu_pyrokinin.fa.aligned.fa +63 -0
  111. data/data/raw_data/npy_npf.fa +20 -0
  112. data/data/raw_data/npy_npf.fa.aligned.fa +40 -0
  113. data/data/raw_data/protostomian_CCAP.fa +14 -0
  114. data/data/raw_data/protostomian_CCAP.fa.aligned.fa +42 -0
  115. data/data/raw_data/protostomian_allatostatinA_buccalin.fa +100 -0
  116. data/data/raw_data/protostomian_allatostatinA_buccalin.fa.aligned.fa +1350 -0
  117. data/data/raw_data/protostomian_leucokinin.fa +18 -0
  118. data/data/raw_data/protostomian_leucokinin.fa.aligned.fa +63 -0
  119. data/data/raw_data/protostomian_tackykinin.fa +504 -0
  120. data/data/raw_data/protostomian_tackykinin.fa.aligned.fa +2002 -0
  121. data/data/raw_data/tachykinin.fa.aligned.fa +13546 -0
  122. data/data/raw_data/vertebrate_ghrelin_motilin.fa +16 -0
  123. data/data/raw_data/vertebrate_ghrelin_motilin.fa.aligned.fa +32 -0
  124. data/lib/neurohmmer.rb +89 -0
  125. data/lib/neurohmmer/arg_validators.rb +71 -0
  126. data/lib/neurohmmer/hmmer.rb +71 -0
  127. data/lib/neurohmmer/output.rb +50 -0
  128. data/lib/neurohmmer/version.rb +4 -0
  129. data/neurohmmer.gemspec +34 -0
  130. data/spec/neurohmmer_spec.rb +11 -0
  131. data/spec/spec_helper.rb +2 -0
  132. data/template/contents.slim +55 -0
  133. metadata +269 -0
data/data/hmm/vertebrate_ghrelin_motilin.fa.hmm ADDED
@@ -0,0 +1,382 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME vertebrate_ghrelin_motilin.fa.aligned
3
+ LENG 120
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:52:11 2015
11
+ NSEQ 8
12
+ EFFN 1.402344
13
+ CKSUM 4240203003
14
+ STATS LOCAL MSV -9.4248 0.71350
15
+ STATS LOCAL VITERBI -10.5595 0.71350
16
+ STATS LOCAL FORWARD -4.1448 0.71350
17
+ HMM A C D E F G H I K L M N P Q R S T V W Y
18
+ m->m m->i m->d i->m i->i d->m d->d
19
+ COMPO 2.50706 4.51476 3.06985 2.54751 3.41332 3.04565 3.83103 2.95025 2.66932 2.32916 3.34331 3.20832 3.13846 2.84203 2.85516 2.59344 2.90890 2.71288 4.96758 3.72544
20
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
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+ 0.01863 4.38810 5.11044 0.61958 0.77255 0.00000 *
22
+ 1 3.47375 4.95422 4.66437 4.32921 3.56145 4.25980 4.94515 2.79632 4.06434 2.10171 0.64705 4.53358 4.74851 4.42377 4.20210 3.86187 3.80294 2.85804 5.45030 4.24835 1 M - - -
23
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+ 0.01863 4.38810 5.11044 0.61958 0.77255 0.48576 0.95510
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+ 2 2.68953 4.27261 3.83486 3.26132 2.82474 3.73014 4.01078 2.67806 3.16721 2.18046 3.36035 3.58423 2.63409 3.44865 2.87219 3.00012 2.92366 1.75307 4.87011 3.65346 2 v - - -
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+ 0.01863 4.38810 5.11044 0.61958 0.77255 0.48576 0.95510
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+ 3 2.67694 4.71244 3.17358 2.68904 4.02569 2.87835 3.83758 3.42854 2.66931 2.30878 3.92025 3.16062 3.94384 2.59150 3.08254 1.63646 2.94793 3.12106 5.35038 4.05292 3 s - - -
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+ 0.01863 4.38810 5.11044 0.61958 0.77255 0.48576 0.95510
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+ 4 2.79950 5.05414 3.17698 2.58500 4.35551 3.57807 3.02703 3.76906 2.08226 3.31204 3.19192 3.08692 2.98168 2.83176 1.69035 2.80701 3.01506 3.42562 5.48449 4.17557 4 r - - -
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+ 0.01863 4.38810 5.11044 0.61958 0.77255 0.48576 0.95510
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+ 5 2.77256 3.42014 3.21446 2.63724 4.30992 2.43772 3.74441 3.71531 1.53274 3.28327 4.10014 3.12365 3.96147 2.88750 2.38842 2.80365 3.00900 3.37362 5.47542 4.17734 5 k - - -
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+ 0.01863 4.38810 5.11044 0.61958 0.77255 0.48576 0.95510
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+ 6 1.79191 4.85500 3.14884 2.62506 4.27874 3.46396 3.79223 3.69149 2.52204 3.28317 4.09503 2.63360 3.92166 2.94313 2.02142 2.73367 2.45118 3.32923 5.49889 4.18347 6 a - - -
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+ 7 2.27312 4.35598 4.28384 3.82993 3.86830 3.67601 4.59478 2.42282 3.74143 2.72985 3.77449 3.95695 4.26824 4.01644 3.97460 3.07871 2.10103 1.09255 5.47285 4.27240 7 v - - -
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+ 8 1.52933 2.96729 3.68951 3.15653 3.67738 2.81726 4.05157 3.04521 3.10526 2.76190 3.64807 3.46845 3.99113 3.39687 3.43353 2.40448 2.88918 2.77678 5.12012 2.98164 8 a - - -
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302
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303
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304
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305
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306
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307
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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340
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341
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342
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343
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344
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
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359
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360
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361
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362
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363
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364
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365
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366
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367
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368
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369
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370
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371
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372
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373
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374
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375
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376
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377
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
378
+ 0.02675 4.03024 4.75259 0.61958 0.77255 0.86422 0.54711
379
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380
+ 2.68630 4.41917 2.77570 2.73094 3.46405 2.40448 3.72545 3.29405 2.67792 2.69406 4.24741 2.90370 2.73629 3.18197 2.89821 2.37835 2.77528 2.98569 4.58272 3.61554
381
+ 0.50016 0.93251 * 1.98956 0.14706 0.00000 *
382
+ //
data/data/raw_data/CRH_DH44.fa ADDED
@@ -0,0 +1,44 @@
1
+ >Uniprot_CRH_Hsap
2
+ MRLPLLVSAGVLLVALLPCPPCRALLSRGPVPGARQAPQHPQPLDFFQPPPQSEQPQQPQARPVLLRMGEEYFLRLGNLNKSPAAPLSPASSLLAGGSGSRPSPEQATANFFRVLLQQLLLPRRSLDSPAALAERGARNALGGHQEAPERERRSEEPPISLDLTFHLLREVLEMARAEQLAQQAHSNRKLMEIIGK
3
+ >gi_62911756_Sauvagine_Psau
4
+ MNLPSSVALLACFLVLLDRSELAPLERSFFHESGPEESARSLLDSDPMKRQGPPISIDLSLELLRKMIEIEKQEKEKQQAANNRLLLDTIGK
5
+ >Uniprot_UCN1_Hsap
6
+ MRQAGRAALLAALLLLVQLCPGSSQRSPEAAGVQDPSLRWSPGARNQGGGARALLLLLAERFPRRAGPGRLGLGTAGERPRRDNPSLSIDLTFHLLRTLLELARTQSQRERAEQNRIIFDSVGK
7
+ >Uniprot_UCN2_Hsap
8
+ MTRCALLLLMVLMLGRVLVVPVTPIPTFQLRPQNSPQTTPRPAASESPSAAPTWPWAAQSHCSPTRHPGSRIVLSLDVPIGLLQILLEQARARAAREQATTNARILARVGHC
9
+ >Uniprot_UCN3_Hsap
10
+ MLMPVHFLLLLLLLLGGPRTGLPHKFYKAKPIFSCLNTALSEAEKGQWEDASLLSKRSFHYLRSRDASSGEEEEGKEKKTFPISGARGGARGTRYRYVSQAQPRGKPRQDTAKSPHRTKFTLSLDVPTNIMNLLFNIAKAKNLRAQAAANAHLMAQIGRKK
11
+ >Ensembl_ENSTRUP00000030463_CRH2_Trub
12
+ MRPTPLLLLLSALLLSSLLRPAAGRPSSLPSWPDELGRLRTQQLEEMLLQAAAAGDSAASELLDDLLLKLFQRRSPELLHLLPVGQEEEAARPVLKRSEEPPLSIDLTFHLLRKMIKEAKMENQKEQELINRKLLDEFGK
13
+ >Ensembl_ENSTRUP00000040554_UCN_Trub
14
+ MLSSLKTLLLLSVLCTPTSSLCLHLSDYRLPLLCDDHMAVGLPGDDDVPGYSPADDWASLLQSAYLSSSSAESSREKRTAAPANYRFLRRTKLRGQMLRNSSKGDRRSRLTLSLDVPTNIMNVLFDVAKAKNLRAKAAENARLLAHIGRRK
15
+ >Ghost_KH.C4.329.v1.A.ND1-1_Cint
16
+ MVLVTVVVFVVLAMSLGVQLVDGKFHVGTSSPLLLDGVALGSLTITDYKEEYAAPAVNRKTRRSPSCCGLHAIPRVKNSIFIQPNRSTTVHLTTRKPALGRNPFLSLDVPLSFLSKLMEVKRREEQRKIAKIKSVHNSSLMKRIGK
17
+ >Ensembl_reftig_15_538821_539886_Csav
18
+ MENSFVCFAVFALVLSRLAGAKSDKLGLSQKIVAIKDDWVVRCAKMQSEIANPLNSWTKRGISLEKTTKVDPISGTDRSPRFRRAAKPKPQTNVLSLDVPLSFLSKLIEMSRREDKRQREKEISLRNKKLMEKYGK
19
+ >gi_187098484_Skow
20
+ MHLCIVIIRFMAVIFVALTVVEANPIHRPSMLSEWLRTLKDENDRDTNIGYREITAFKRNPTSGHSIGLSLDIIRDRLEKAESERMQQEKQSDINRYRQNTELMTGLGRRRRSMEEVYRQ
21
+ >gi_155729_Egg-laying_hormone_Acal
22
+ MKRPNNRPTNTMSLILCLTLSSLCVMSQSASVHGKNFATNRAVKSSSPFVVLSPDDNVVSMSGENGYRSALREAFDKSSRDYDDNGEDVFSNEKRRLRFHKRRLRFDRRDQDEGNFRRFPTNAVSMSADENSPFDLSNEDGAVYQRDLRAPRLRFYSLRKRAAGEMEQSEGQNPETESHSRRKRSVLTPSLSSLGESLESGISKRISINQDLKAITDMLLTEQIRERQRYLADLRPRLLEKGKRSSGVSLLTSNKDEEQRELLKAISNLLD
23
+ >jgi_169597_Lgig
24
+ MTSYAMPRSYSQVPEELSSQDQSRDYYEPLNAILHRLRELILMQPHSLRETIRYTQITPTTPIPIAMKKRSRLSINQELKSLANLLVLRENKRREAQKTKLRSKLLSIGKRSMPQNQDRDHVIEETPVSDRDMFLTELFAEISEQEMTYVLGQVLGSEIAAKGGNEYQGQERLPYEI
25
+ >jgi_sca_87:656961-669122_Lgig
26
+ MEWNMNKSLSVLVLCLFIFVVDDAHSYSMNRKSESSRHIRSASDIPDDRIQDSKASFHENYFGTDPDHQNLYRERLESMFSDQKKRMDIHQQQVSLKNLINLIHETSNRIRKLSKTERPDMDDDENVRIKTVVKTWSKNDPENGRDNVISGYKTEVGNPKRAGRLSINGALSSLADLLVSENQRRDRLESMELRQRLQYLG
27
+ >gi_260927617_Cgig
28
+ MKMKLNVMAVIVTALFVSVDAFILQDQDNQPDLSEADSIPVEKRGRLSLTADLRSLARMLEAHRKRFIASRFPYDSIRKKLFRYGKRSPVTETLEYNEGEDRSNALDSEFPSVKVEEESPIYNIKRQRLSVNGALSSLADMLAANGRQRMMSEMAMNRQRLFGLG
29
+ >gi_144925239_Lymnaea_stagnalis
30
+ MKMSGLLSKPDYGVVGIVFTVVFCCWCSSSTTHALSIAEPGRDRYDKRSPTGHGVEVVEVAQSGEDYGSNRPQPVYGDEDEEDSADVYVGSDESSSGEKTRLTAAKRRLRFNKRRLRASKRRLRFHKRRVDSADESNDDGFDRKAREPRLRFHDVRKRSVTAEEGSENAEIEESHLGNSRSRRSADSAPSSANEVQRFKRLSITNDLRAIADSYLYDQHKLRERQEENLRRRFLELGKRGSAFFDHIPIIFGEPQYDYQPFK
31
+ >gi_213134317_Hmel
32
+ MMWWAIWCAVVVAGSAGTHAAPSSNMIPSAIDWTQFDALAPEDDSLGYAVSPMSRRSAAGSPRLYLLAEVPRDSQNLAELREGRPRPKRKMPPLSINNPMEVLRQRLLLEVARKQMREANQRQAVANRVFLQNVGKRGFWAGSAPRYDN
33
+ >Ensembl_FBtr0082080_DH44_Dmel
34
+ MMKATAWFCPVLLTLLCATRLVCTAQRGAVGAGGAAGGSGAAAGGAEVGGSGRTNGYPLDYPDGTRNSQDDFLLAKRNKPSLSIVNPLDVLRQRLLLEIARRQMKENSRQVELNRAILKNVGKRVVLRGGGGGGGSGAGGLAPKVSRRYRQQWPVERELERERQRERERERDAVREEQLDRQQLLPWKHFPSQLWSYGWALSPYKESSQLQFADSQQSASTGPQSQALPKQLQLLSYAKKPLDVAGMSLARHRVSGNEANETNHENDDGNGASKNPARYVDDGDNEGEDSYNDVGTEGVGLGLGMGVGLGLERFEVLEDKPNWANEEPNELVVVNANDRVPWSFPYRFHKSQHNVN
35
+ >jgi_95468_Dpul
36
+ MRWHVATLAAVWLIIMGWCGSAVMGQPIAGSMDQPHPAHHPPAGQTIPEMWALMDPADGPPDTIRDGDDLNGDLYYFPAVPIMKRQQSLDDDSGWISQDRSKRQSQSHSGSSGNHHSQLSIISPIEALRSRLRLEMLRRQYGNQIKQNQDKLERVGKRRKRSDQSSPIAVDGSDEKRMSQPSVAPAAIKAP
37
+ >gi_125487989_Isca
38
+ MRCAQSSHPLLRPWLLLALLVTDAALGARLGGSKASLDLSDLWKRGPLSLRSRGPVPSLSMHSRDHMPSLSIVSPLDVLRDKMMQDIIERSIKNKIQANDKILKDLGKRSAPPAAIGEDVAVSLLRRDDDRSSFSPQESFSDELL
39
+ >gi_300043228_Apis
40
+ MRILTIAWILVAVTWCCDSAVIYDPVVQNTRYYEPRIQDLELLDKNFFDMASIEKRNGAMQGESPRSRPSLSIVNSLDVLRQKLMYEVARRHVDENQKVLSQNHQILKNLGKRSLFPFIEVPRRYNVFRI
41
+ >gi_282199930_(partial)_Turt
42
+ TDGYLQNLLNEYRQKQGSINLRHWVRGVSPPRLSVTSPIAVLRDALMEEIKRKKIQETQAKIALNEKILKEVG
43
+ >gi_164433160_Oarc
44
+ MIECPQKTFNGINNLVNLRRSSKFSWTLISLILMITLACVLESSTVVSSPIKSKSRRDHSHHHHHHHHHHRQSRNHTKHHRIPEILEQPVPDSSGSLSIVGPLDVLRQNMLMEMHKTRVRHAKNKIVESNREYLERIGR
data/data/raw_data/CRH_DH44.fa.aligned.fa ADDED
@@ -0,0 +1,242 @@
1
+ >Uniprot_CRH_Hsap
2
+ -MRLP-----------------------LLVSAGVLLVALLPCPPCRALLSRGPVPG-AR
3
+ QAPQHPQPLDFFQ-------PPPQSEQPQQPQARPVLLRMGEEY---FLRLGNLNKSPAA
4
+ PLSPASSLLAGG--SGSRPSPEQATANFFRVLLQQLLLPRRSLD----------------
5
+ ----------------------------------SPAALAERGARNALGGHQE-------
6
+ ----APERERRS------------------EEPPISLDLTFHLLREVL---EMARAEQLA
7
+ QQAHS----NRKLMEIIGK-----------------------------------------
8
+ ------------------------------------------------------------
9
+ ------------------------------------------------------------
10
+ ------------------------------------------------------------
11
+ ------------
12
+ >gi_62911756_Sauvagine_Psau
13
+ -MNLP----------------SSVAL---LACFLVLL----------------------D
14
+ RSELAPLERSF-------------------------------------------------
15
+ ------------------------------------------------------------
16
+ ----------------------------------FHESGPEESARSLLD-----------
17
+ -----SDPMKRQ-------------------GPPISIDLSLELLRKMI---EIEKQEKEK
18
+ QQAAN----NRLLLDTIGK-----------------------------------------
19
+ ------------------------------------------------------------
20
+ ------------------------------------------------------------
21
+ ------------------------------------------------------------
22
+ ------------
23
+ >Uniprot_UCN1_Hsap
24
+ -MRQAGRA--------------------ALLAALLLLVQLC-----------------PG
25
+ SSQRSPEAAGV--------------QDPS-------------------LRWSPGARNQG-
26
+ --------------GGARA----------LLLLLAERFPRRAGP----------------
27
+ ----------------------------------GRLGLGTAGERP--------------
28
+ ---------RRD-------------------NPSLSIDLTFHLLRTLL---ELARTQSQR
29
+ ERAEQ----NRIIFDSVGK-----------------------------------------
30
+ ------------------------------------------------------------
31
+ ------------------------------------------------------------
32
+ ------------------------------------------------------------
33
+ ------------
34
+ >Uniprot_UCN2_Hsap
35
+ -MTRC-------------------AL--LLLMVLMLGRVLVVPVTPIPTFQLRP----QN
36
+ SPQTTP------------------------------------------------------
37
+ ------------------------------------------------------------
38
+ ----------------------------------RPAASESPSAAPTWPWAAQ-------
39
+ ----SHCSPTRH----------------PGSRIVLSLDVPIGLLQILL---EQARARAAR
40
+ EQATT----NARILARVGH-----------------------------------------
41
+ ------------------------------------------------------------
42
+ ------------------------------------------------------------
43
+ ------------------------------------------------------------
44
+ -----------C
45
+ >Uniprot_UCN3_Hsap
46
+ -MLMP-------------------------VHFLLLLLLLLGGPRTGLP---------HK
47
+ FYKAKPIFSCLNT--ALSEAEKGQWEDASLLSKRSFH----------YLRSRDASSGEEE
48
+ EGKEKKTFPISGARGGARG--------------TRYRYVSQAQP----------------
49
+ ----------------------------------RGKPRQDTAKSP--------------
50
+ ---------HRT-------------------KFTLSLDVPTNIMNLLF---NIAKAKNLR
51
+ AQAAA----NAHLMAQIGRKK---------------------------------------
52
+ ------------------------------------------------------------
53
+ ------------------------------------------------------------
54
+ ------------------------------------------------------------
55
+ ------------
56
+ >Ensembl_ENSTRUP00000030463_CRH2_Trub
57
+ -MRPT-------------------PL--LLLLSALLLSSLLRPAAGR-----------PS
58
+ SLPSWPDELGR-------------------------------------LRTQQLEEMLLQ
59
+ AAA-----------AGDSA------ASELLDDLLLKLFQRRSPELLHL------------
60
+ ----------------------------------LPVGQEEEAARPVL------------
61
+ ---------KRS------------------EEPPLSIDLTFHLLRKMI---KEAKMENQK
62
+ EQELI----NRKLLDEFGK-----------------------------------------
63
+ ------------------------------------------------------------
64
+ ------------------------------------------------------------
65
+ ------------------------------------------------------------
66
+ ------------
67
+ >Ensembl_ENSTRUP00000040554_UCN_Trub
68
+ -MLSS-------------------------LKTLLLLSVLCTPTSSLCL---------HL
69
+ SDYRLPLLCDDHM--AVGL--PGDDDVPGYSPADDWAS---------LLQSAYLSSSSAE
70
+ SSREKRTAAPAN-----------------------YRFLRRTKL----------------
71
+ ----------------------------------RGQMLRNSSKGD--------------
72
+ ---------RRS-------------------RLTLSLDVPTNIMNVLF---DVAKAKNLR
73
+ AKAAE----NARLLAHIGRRK---------------------------------------
74
+ ------------------------------------------------------------
75
+ ------------------------------------------------------------
76
+ ------------------------------------------------------------
77
+ ------------
78
+ >Ghost_KH.C4.329.v1.A.ND1-1_Cint
79
+ -MVLV-----------------------TVVVFVVLAMSLGVQLVDGK----------FH
80
+ VGTSSPLLLDG-V--ALGS-----------------------------LTITDYKEEYAA
81
+ PAVNRKT--------------------------------RRSPSCCGLHA----------
82
+ ---------I------------PRVKNSIFIQPNRSTTVHLTTRKPAL------------
83
+ ---------GRN--------------------PFLSLDVPLSFLSKLM---EVKRREEQR
84
+ KIAKIKSVHNSSLMKRIGK-----------------------------------------
85
+ ------------------------------------------------------------
86
+ ------------------------------------------------------------
87
+ ------------------------------------------------------------
88
+ ------------
89
+ >Ensembl_reftig_15_538821_539886_Csav
90
+ -MENS------------------------FVCFAVFALVL------------------SR
91
+ LAGAKSDKLGL--------------SQKIVAIKDDWV-----------VRCAKMQSEIAN
92
+ P-----------------------------------------------------------
93
+ ----------------------------LNSWTKRGISLEKTTKVDPISGTDR-------
94
+ -----SPRFRRA-------------AKPKPQTNVLSLDVPLSFLSKLI---EMSRREDKR
95
+ QREKEISLRNKKLMEKYGK-----------------------------------------
96
+ ------------------------------------------------------------
97
+ ------------------------------------------------------------
98
+ ------------------------------------------------------------
99
+ ------------
100
+ >gi_187098484_Skow
101
+ -MHLC---------I------------VIIRFMAVIFVALTVV---------------EA
102
+ NPIHRPSMLSE------------------------------------WLRTLKDENDRDT
103
+ N-------------IGYRE-----------------------------------------
104
+ ------------------------------------------------------------
105
+ -----ITAFKRN------------------PTSGHSIGLSLDIIRDRLEKAESERMQQEK
106
+ QSDINRYRQNTELMTGLGRRR---------------------------------------
107
+ ------------------------------------------------------------
108
+ -----------------------------------------------------RS-----
109
+ -------------------------MEEVYRQ----------------------------
110
+ ------------
111
+ >gi_155729_Egg-laying_hormone_Acal
112
+ -MKRP-------------NNRPTNTM---SLILCLTLSSLCVMSQSASVHGKNFATN-RA
113
+ VKSSSPFVVLS------------PDDNVVSMSGENGYRSALR------EAFDKSSRDYDD
114
+ N--------------GEDV--FSNEKRRLRFHKRRLRFDRRDQDEGNFRRFPTNAVSMSA
115
+ DENSPFDLSNEDGAVYQRDLRAPRLR--FYSLRKRAAGEMEQSEGQNPETES--------
116
+ -----HSRRKRSVLTPSLSSLG--ESLESGISKRISINQDLKAITDMLLT-EQIRERQRY
117
+ LAD------LRPRLLEKGKRSSGVSL----------------------------------
118
+ --LTSNKDEEQRE-------------------------LLKAISNL-----------L--
119
+ -----------------------------------------------------------D
120
+ ------------------------------------------------------------
121
+ ------------
122
+ >jgi_169597_Lgig
123
+ -MTSY-------------------AM--------------------------------PR
124
+ SYSQVPEE----------------------------------------LSSQDQSRDYYE
125
+ P--------------------LNAILHRLRELILMQPHSLRETI----------------
126
+ ----------------------------------RYTQITPTTPIP--------------
127
+ -----IAMKKRS---------------------RLSINQELKSLANLLVLRENKRREAQK
128
+ TK-------LRSKLLSIGKRSMPQNQD---RDHVIEETPV--------------------
129
+ ----SDRDMFLTE-------------------------LFAEISE------QEMTYVLGQ
130
+ VLGSEI-----------------------------------------AAKGGNEY-----
131
+ -QGQE---------------------RLPYEI----------------------------
132
+ ------------
133
+ >jgi_sca_87:656961-669122_Lgig
134
+ -MEWNMNK-------------------SLSVLVLCLFIFVVDDAHSYSMNRKSESSRHIR
135
+ SASDIPD-----------------------------------------DRIQDSKASFHE
136
+ NY------------FGTDP--DHQNLYRERLESMFSDQKKRMDI----------------
137
+ ---------------HQQQVSLKNLINLIHETSNRIRKLSKTERPDMDDDENVRIKTVVK
138
+ TWSKNDPENGRDNVISGYKT----EVGNPKRAGRLSINGALSSLADLLVS-ENQRRDRLE
139
+ SME------LRQRLQYLG------------------------------------------
140
+ ------------------------------------------------------------
141
+ ------------------------------------------------------------
142
+ ------------------------------------------------------------
143
+ ------------
144
+ >gi_260927617_Cgig
145
+ -MKMK------------------------LNVMAVIVTALFVSVDAFILQDQDNQPD-LS
146
+ EADSIPVEKRG------------------------------------RLSLTADLRSLAR
147
+ MLEAHRKRFIAS-RFPYDS-----------IRKKLFRYGKRSPVTETLE-----------
148
+ ----------------------------YNEGEDRSNALDSEFPSVKVEEESP-------
149
+ -----IYNIKRQ---------------------RLSVNGALSSLADMLA--ANGRQRMMS
150
+ EMAM-----NRQRLFGLG------------------------------------------
151
+ ------------------------------------------------------------
152
+ ------------------------------------------------------------
153
+ ------------------------------------------------------------
154
+ ------------
155
+ >gi_144925239_Lymnaea_stagnalis
156
+ -MKMS-----------GLLSKPDYGV--VGIVFTVVFCCWCSSSTTHALSIAEPGRD--R
157
+ YDKRSPTGHGV-------------EVVEVAQSGEDYGSNRPQ-----PVYGDEDEEDSAD
158
+ VYVGSDESS-----SGEKTR-LTAAKRRLRFNKRRLRASKRRLR---FHKRRVD----SA
159
+ DE------SNDDG--FDRKAREPRLR--FHDVRKRSVTAEEGSENAEIEESHL-------
160
+ ----GNSRSRRSADSAPSS------ANEVQRFKRLSITNDLRAIADSYLY-DQHKLRERQ
161
+ EEN------LRRRFLELGKRGSA-------------------------------------
162
+ --------------------------------------FFDHI---------------PI
163
+ IFGEP------------------------------------------------QY----D
164
+ --------------------------YQPFK-----------------------------
165
+ ------------
166
+ >gi_213134317_Hmel
167
+ MMWWA-------------------IW---------CAVVVAGSAGTHA----------AP
168
+ SSNMIPSAIDWTQFDALAP-EDDSLGYAVSPMSRRSAAGSPRLYL--LAEVPRDSQNLAE
169
+ L-----------------------------------------------------------
170
+ ------------------------------------------------------------
171
+ --REGRPRPKRK-------------------MPPLSINNPMEVLRQRLLL-EVARKQMRE
172
+ ANQRQ-AVANRVFLQNVGKRGFWAGS-----------AP---------------------
173
+ ------------------------------------------------------------
174
+ -----------------------------------------------------RY----D
175
+ N-----------------------------------------------------------
176
+ ------------
177
+ >Ensembl_FBtr0082080_DH44_Dmel
178
+ MMKAT-------------------AWFCPVLLTLLCATRLVCTAQRGAVGAGGAAGG---
179
+ -------------------------SGAAAGGAEVGGSGRTNGY---PLDYPDGTRNSQD
180
+ D-----------------------------------------------------------
181
+ ------------------------------------------------------------
182
+ -----FLLAKRN-------------------KPSLSIVNPLDVLRQRLLL-EIARRQMKE
183
+ NSRQ--VELNRAILKNVGKRVVLRGGGGGGGSGAGGLAPKVSRRYRQQWPVERELERERQ
184
+ RERERERDAVREEQLDRQQLLPWKHFPSQLWSYGWALSPYKESSQLQFADSQQSASTGPQ
185
+ SQALPKQLQLLSYAKKPLDVAGMSLARHRVSGNEANETNHENDDGNGASKNPARYVDDGD
186
+ NEGEDSYNDVGTEGVGLGLGMGVGLGLERFEVLEDKPNWANEEPNELVVVNANDRVPWSF
187
+ PYRFHKSQHNVN
188
+ >jgi_95468_Dpul
189
+ -MRWHVATLAA-------------VW---LIIMGWCGSAVMGQPIAGSMDQPHPAHH-PP
190
+ AGQTIPEMWAL----------MDPADGPPDTIRDGDDLNGDLYYFP-AVPIMKRQQSLDD
191
+ D-------------SGWIS-----------------------------------------
192
+ ------------------------------------------------------------
193
+ -----QDRSKRQ--SQSHS------GSSGNHHSQLSIISPIEALRSRLRL-EMLRRQYGN
194
+ QIKQ-----NQDKLERVGKRRKRSDQS----------SPI--------------------
195
+ --AVDGSDEKRMSQ----------------------------------------PSVAPA
196
+ AIKAP-------------------------------------------------------
197
+ ------------------------------------------------------------
198
+ ------------
199
+ >gi_125487989_Isca
200
+ -MRCAQSS-------------------HPLLRPWLLLALLVTDAALGA------------
201
+ -----------------------------------------------RLGGSKASLDLSD
202
+ L-----------------------------------------------------------
203
+ -------------------------------WKRGPLSLRSRGPVP--------------
204
+ ----SLSMHSRD------------------HMPSLSIVSPLDVLRDKMMQ-DIIERSIKN
205
+ KIQA-----NDKILKDLGKRS----------------AP---------------------
206
+ ----------------------------------------------------------PA
207
+ AIGEDVAVSLL------------------------------------------RR---DD
208
+ DRSSFS-------------------PQESFSD-------------ELL------------
209
+ ------------
210
+ >gi_300043228_Apis
211
+ -MRIL------------------------TIAWILVAVTWCC----------------DS
212
+ AVIYDPVVQNT------------------------------RYYEPRIQDLELLDKNFFD
213
+ M-----------------------------------------------------------
214
+ ------------------------------------------------------------
215
+ -----ASIEKRN---------GAMQGESPRSRPSLSIVNSLDVLRQKLMY-EVARRHVDE
216
+ NQKV--LSQNHQILKNLGKRSLF-------------------------------------
217
+ --------------------------------------PFIEVPR---------------
218
+ -----------------------------------------------------RY-----
219
+ ---------------------------NVFRI----------------------------
220
+ ------------
221
+ >gi_282199930_(partial)_Turt
222
+ ------------------------------------------------------------
223
+ ------------------------------------------------------------
224
+ ------------------------------------------------------------
225
+ ----------TDG--YLQNL----LN----------------------------------
226
+ -----EYRQKQGSINLRHWVRGV-------SPPRLSVTSPIAVLRDALME-EIKRKKIQE
227
+ TQAK--IALNEKILKEVG------------------------------------------
228
+ ------------------------------------------------------------
229
+ ------------------------------------------------------------
230
+ ------------------------------------------------------------
231
+ ------------
232
+ >gi_164433160_Oarc
233
+ MIECPQKTFNGINNLVNLRRSSKFSW---TLISLILMITLACVLESSTV-----------
234
+ ------------------------------------------------VSSPIKSKSRRD
235
+ HSHHHHHHH---------------------------------------------------
236
+ ------------------------------------------------------------
237
+ ----HHHRQSRN-HTKHHRIPEILEQPVPDSSGSLSIVGPLDVLRQNMLM-EMHKTRVRH
238
+ AKNKI-VESNREYLERIGR-----------------------------------------
239
+ ------------------------------------------------------------
240
+ ------------------------------------------------------------
241
+ ------------------------------------------------------------
242
+ ------------