neurohmmer 0.1.0
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- checksums.yaml +7 -0
- data/.gitignore +35 -0
- data/CODE_OF_CONDUCT.md +13 -0
- data/Gemfile +4 -0
- data/LICENSE +662 -0
- data/README.md +136 -0
- data/Rakefile +17 -0
- data/bin/neurohmmer +69 -0
- data/data/hmm/CRH_DH44.fa.hmm +427 -0
- data/data/hmm/Chordate_Glucagon_PACAP.fa.hmm +484 -0
- data/data/hmm/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa.hmm +526 -0
- data/data/hmm/Deutrostomian_tachykinin.fa.hmm +367 -0
- data/data/hmm/Gastrin_releasing_peptide.fa.hmm +448 -0
- data/data/hmm/GnRH.fa.hmm +370 -0
- data/data/hmm/Hypocretin_orexin.fa.hmm +451 -0
- data/data/hmm/Lophotrochozoan_luqin_arthropod_RYamide.fa.hmm +385 -0
- data/data/hmm/NPFF.fa.hmm +430 -0
- data/data/hmm/NPS.fa.hmm +790 -0
- data/data/hmm/PTH.fa.hmm +502 -0
- data/data/hmm/Protostomian_Allatostatin_B.fa.hmm +835 -0
- data/data/hmm/Protostomian_CCH_amide.fa.hmm +415 -0
- data/data/hmm/Protostomian_Ecdysis_Triggering_Hormone.fa.hmm +433 -0
- data/data/hmm/Protostomian_PDF.fa.hmm +265 -0
- data/data/hmm/Protostomian_allatostatin_C.fa.hmm +352 -0
- data/data/hmm/Protostomian_proctolin.fa.hmm +346 -0
- data/data/hmm/Putative_chordate_Opioid.fa.hmm +802 -0
- data/data/hmm/SIF.fa.hmm +286 -0
- data/data/hmm/TRH.fa.hmm +910 -0
- data/data/hmm/allatotropin.fa.hmm +433 -0
- data/data/hmm/ambulacrarian_amphioxus_NPS-like.fa.hmm +847 -0
- data/data/hmm/avp.fa.hmm +475 -0
- data/data/hmm/calcitonin_DH31.fa.hmm +418 -0
- data/data/hmm/cholecystokinin_sulfakinin.fa.hmm +433 -0
- data/data/hmm/chordate_OX26_QRFP.fa.hmm +475 -0
- data/data/hmm/chordate_somatostatin_cortistatin_like.fa.hmm +361 -0
- data/data/hmm/f_type_SALMF.fa.hmm +811 -0
- data/data/hmm/galanin.fa.hmm +391 -0
- data/data/hmm/l_type_SALMF.fa.hmm +523 -0
- data/data/hmm/nmu_pyrokinin.fa.hmm +424 -0
- data/data/hmm/npy_npf.fa.hmm +301 -0
- data/data/hmm/protostomian_CCAP.fa.hmm +415 -0
- data/data/hmm/protostomian_allatostatinA_buccalin.fa.hmm +706 -0
- data/data/hmm/protostomian_leucokinin.fa.hmm +511 -0
- data/data/hmm/protostomian_tackykinin.fa.hmm +760 -0
- data/data/hmm/tachykinin.fa.hmm +541 -0
- data/data/hmm/vertebrate_ghrelin_motilin.fa.hmm +382 -0
- data/data/raw_data/CRH_DH44.fa +44 -0
- data/data/raw_data/CRH_DH44.fa.aligned.fa +242 -0
- data/data/raw_data/Chordate_Glucagon_PACAP.fa +18 -0
- data/data/raw_data/Chordate_Glucagon_PACAP.fa.aligned.fa +72 -0
- data/data/raw_data/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa +10 -0
- data/data/raw_data/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa.aligned.fa +25 -0
- data/data/raw_data/Deutrostomian_tachykinin.fa +1283 -0
- data/data/raw_data/Deutrostomian_tachykinin.fa.aligned.fa +5707 -0
- data/data/raw_data/Gastrin_releasing_peptide.fa +12 -0
- data/data/raw_data/Gastrin_releasing_peptide.fa.aligned.fa +25 -0
- data/data/raw_data/GnRH.fa +22 -0
- data/data/raw_data/GnRH.fa.aligned.fa +66 -0
- data/data/raw_data/Hypocretin_orexin.fa +14 -0
- data/data/raw_data/Hypocretin_orexin.fa.aligned.fa +49 -0
- data/data/raw_data/Lophotrochozoan_luqin_arthropod_RYamide.fa +26 -0
- data/data/raw_data/Lophotrochozoan_luqin_arthropod_RYamide.fa.aligned.fa +91 -0
- data/data/raw_data/NPFF.fa +16 -0
- data/data/raw_data/NPFF.fa.aligned.fa +48 -0
- data/data/raw_data/NPS.fa +8 -0
- data/data/raw_data/NPS.fa.aligned.fa +24 -0
- data/data/raw_data/PTH.fa +24 -0
- data/data/raw_data/PTH.fa.aligned.fa +144 -0
- data/data/raw_data/Protostomian_Allatostatin_B.fa +17 -0
- data/data/raw_data/Protostomian_Allatostatin_B.fa.aligned.fa +120 -0
- data/data/raw_data/Protostomian_CCH_amide.fa +24 -0
- data/data/raw_data/Protostomian_CCH_amide.fa.aligned.fa +72 -0
- data/data/raw_data/Protostomian_Ecdysis_Triggering_Hormone.fa +24 -0
- data/data/raw_data/Protostomian_Ecdysis_Triggering_Hormone.fa.aligned.fa +84 -0
- data/data/raw_data/Protostomian_PDF.fa +16 -0
- data/data/raw_data/Protostomian_PDF.fa.aligned.fa +32 -0
- data/data/raw_data/Protostomian_allatostatin_C.fa +28 -0
- data/data/raw_data/Protostomian_allatostatin_C.fa.aligned.fa +56 -0
- data/data/raw_data/Protostomian_proctolin.fa +16 -0
- data/data/raw_data/Protostomian_proctolin.fa.aligned.fa +32 -0
- data/data/raw_data/Putative_chordate_Opioid.fa +8 -0
- data/data/raw_data/Putative_chordate_Opioid.fa.aligned.fa +32 -0
- data/data/raw_data/SIF.fa +28 -0
- data/data/raw_data/SIF.fa.aligned.fa +70 -0
- data/data/raw_data/TRH.fa +10 -0
- data/data/raw_data/TRH.fa.aligned.fa +50 -0
- data/data/raw_data/allatotropin.fa +31 -0
- data/data/raw_data/allatotropin.fa.aligned.fa +90 -0
- data/data/raw_data/ambulacrarian_amphioxus_NPS-like.fa +8 -0
- data/data/raw_data/ambulacrarian_amphioxus_NPS-like.fa.aligned.fa +24 -0
- data/data/raw_data/avp.fa +28 -0
- data/data/raw_data/avp.fa.aligned.fa +70 -0
- data/data/raw_data/calcitonin_DH31.fa +36 -0
- data/data/raw_data/calcitonin_DH31.fa.aligned.fa +126 -0
- data/data/raw_data/cholecystokinin_sulfakinin.fa +28 -0
- data/data/raw_data/cholecystokinin_sulfakinin.fa.aligned.fa +84 -0
- data/data/raw_data/chordate_OX26_QRFP.fa +10 -0
- data/data/raw_data/chordate_OX26_QRFP.fa.aligned.fa +25 -0
- data/data/raw_data/chordate_somatostatin_cortistatin_like.fa +10 -0
- data/data/raw_data/chordate_somatostatin_cortistatin_like.fa.aligned.fa +20 -0
- data/data/raw_data/f_type_SALMF.fa +118 -0
- data/data/raw_data/f_type_SALMF.fa.aligned.fa +590 -0
- data/data/raw_data/galanin.fa +93 -0
- data/data/raw_data/galanin.fa.aligned.fa +552 -0
- data/data/raw_data/kisspeptin.fa +16 -0
- data/data/raw_data/kisspeptin.fa.aligned.fa +0 -0
- data/data/raw_data/l_type_SALMF.fa +68 -0
- data/data/raw_data/l_type_SALMF.fa.aligned.fa +170 -0
- data/data/raw_data/nmu_pyrokinin.fa +18 -0
- data/data/raw_data/nmu_pyrokinin.fa.aligned.fa +63 -0
- data/data/raw_data/npy_npf.fa +20 -0
- data/data/raw_data/npy_npf.fa.aligned.fa +40 -0
- data/data/raw_data/protostomian_CCAP.fa +14 -0
- data/data/raw_data/protostomian_CCAP.fa.aligned.fa +42 -0
- data/data/raw_data/protostomian_allatostatinA_buccalin.fa +100 -0
- data/data/raw_data/protostomian_allatostatinA_buccalin.fa.aligned.fa +1350 -0
- data/data/raw_data/protostomian_leucokinin.fa +18 -0
- data/data/raw_data/protostomian_leucokinin.fa.aligned.fa +63 -0
- data/data/raw_data/protostomian_tackykinin.fa +504 -0
- data/data/raw_data/protostomian_tackykinin.fa.aligned.fa +2002 -0
- data/data/raw_data/tachykinin.fa.aligned.fa +13546 -0
- data/data/raw_data/vertebrate_ghrelin_motilin.fa +16 -0
- data/data/raw_data/vertebrate_ghrelin_motilin.fa.aligned.fa +32 -0
- data/lib/neurohmmer.rb +89 -0
- data/lib/neurohmmer/arg_validators.rb +71 -0
- data/lib/neurohmmer/hmmer.rb +71 -0
- data/lib/neurohmmer/output.rb +50 -0
- data/lib/neurohmmer/version.rb +4 -0
- data/neurohmmer.gemspec +34 -0
- data/spec/neurohmmer_spec.rb +11 -0
- data/spec/spec_helper.rb +2 -0
- data/template/contents.slim +55 -0
- metadata +269 -0
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