bio-1.1.0

https://rubygems.org

id: 11282

number: 1.1.0

platform: ruby

spec_sha256: a602aaace95e4a68cc281dbd2e74aa073d284f0be84b00b685318fe0b21472e0

sha256: 2367c8e2eb44643e068b2eaf53dc0c730b27d16ab22d8dda8fe8af3ca419cbc3

created_at: 2024-05-13 08:13:57 UTC

updated_at: 2024-05-23 19:20:22 UTC

position: 19

version_data_entries_count: 328

uploaded_at: 2009-07-25 18:31:35 UTC

indexed: true

has_extensions:

extensions:

Gem size: 762 KB

Version Data Entries

Total: 328

Unpacked size: 2.78 MB

Full Name	Mode	Size	SHA
lib/bio/appl/muscle.rb	644	1.37 KB	3913777ac7be3249cd810bc9718b5cad5c33f1baf8b81f86176551db71436bc5
lib/bio/appl/phylip/alignment.rb	644	3.36 KB	74ab9a941fc46def4555c416d5502eaf884d8fe7da4499b14a57df98c5d15ec2
lib/bio/db/kegg/keggtab.rb	644	8.86 KB	8746e7d99d099528bb6c32cd2b15f075d7b51a6c6f1afc515e72a29886d7555e
lib/bio/shell/plugin/seq.rb	644	6.53 KB	5c21f7ae85dbda5c18c954a9ac27980659b02d7cd27020f78ba3814e2a50d232
lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-gem.png	644	6.79 KB	483e2f19ce8966c8490191c261d40e3bafcff790c1abdf21060307e31ef2372d
lib/bio/util/restriction_enzyme/analysis.rb	644	9.58 KB	ce30016b52ee7520e2cba5d83363c057a72a664c84f9a42a6fb2dd2a9fcb596f
lib/bio/shell/web.rb	644	2.18 KB	2075a224e814a0e8dd336dbaf323a7e3a3b8a0e49fbca169e8221a0c229ae123
doc/Changes-0.7.rd	644	12.6 KB	abbb3f93d8667d7f65d656454ddc93715adc55de6e9771fb9082542b120dbb94
lib/bio/db/pdb/chemicalcomponent.rb	644	6.67 KB	498ea530e871471899667b03b944151b291d662c51b0732a44ace5386f492211
lib/bio/appl/bl2seq/report.rb	644	11.3 KB	3ca1ec254b043913e319665db79a256ab5c49241ea27cfd49a3bccabd0854888
lib/bio/appl/gcg/msf.rb	644	5.15 KB	fd778a350e36e6e4df600f44dbae2a78628aa0eb6d3c2de95cfb895b403ac601
lib/bio/db/embl/swissprot.rb	644	1014 Bytes	a48b17fc793812516ddf692232b14e62e0f87bd8a9dfe3a5631eda69a5848ae3
lib/bio/db/kegg/reaction.rb	644	1.17 KB	c6554182d498469e395ebe83f60a8d09a7a3a6b920c9275d87c6d5c2eda22f21
lib/bio/db.rb	644	8.14 KB	63ef9fcaf06e37eb4e88d3040881f7689d6f99b9e75cf8f2824f8b82ff9e38d4
lib/bio/sequence/generic.rb	644	428 Bytes	40ebce47a9323f96fa8e8428aa20cbcbebdd34b52ebbe9547cacb22c98f33b30
lib/bio/shell/plugin/entry.rb	644	2.68 KB	2df7619a4e89724c6606c03b8c44dd7b8161c8ce72ee4992303f3753e5d6ba3a
lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css	644	4.87 KB	6f6b585db4cb21d8273eec47dd83f97b3c47d0887c988f2840731142aa1458c3
lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml	644	1.2 KB	45ae9643b004995d4d33c18c12bcd2fb412b786b4d8f05f0ae2f7670bf519305
lib/bio/shell/script.rb	644	476 Bytes	5be184d23bb6de666291ff4bfefdd1293d1dbc5cacd63b00ac8c3124e3322c90
sample/any2fasta.rb	644	1.33 KB	2b781b7bdf098238d5fe0772f5cabeae4130d09755ba1c8f9fa05d9cd9338a32
sample/fsplit.rb	644	1.11 KB	400c70b8905f27f74fd581c8c9accf5ab24748c9725131890d3e8a560dd4b80b
sample/genome2rb.rb	644	910 Bytes	c163eac8c0477dd2b7f93400518da3f656d11de834693f82c432add97876cb06
sample/psortplot_html.rb	644	4.95 KB	75a7811ea4d6aa05206b50aaea0643dc7d2d9b3813955d1d84904f227a9ceafb
test/data/embl/AB090716.embl	644	2.47 KB	0cf0a12b44f6472a021abcf4dc38f2f8a64d6dd4049463056057968e2ce0f0f4
test/data/iprscan/merged.txt	644	5.17 KB	b8920e4a017e8c9d0bdd837bf6691c8ed13fe3dfad8f5992b97cdb1f4db62b8c
test/unit/bio/db/embl/test_embl.rb	644	4.9 KB	004a8c4bc1ae3ca016ab7e910980ee63e81af358822ecfd224003a8d2624fae2
test/unit/bio/db/embl/test_embl_rel89.rb	644	5.09 KB	023de5ae37c659b2ae482df98114dfd174f3920acf11cc8bb257bd98e1c1c69d
test/unit/bio/db/test_aaindex.rb	644	6.05 KB	8798d4d41b60393aa3e42329b84a1618a84d36df213c50bec2121389ed9b8377
test/unit/bio/db/test_lasergene.rb	644	8.35 KB	6e66af40738d72e98689c6dfbba10437b5e2a905f4df486a9a7ddf8c32db3c6c
test/unit/bio/io/test_ensembl.rb	644	2.4 KB	6d21a47a430f655fde25adcb3d7888788825bf5d607069ab9fa0789c4442440a
test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb	644	1.27 KB	49aeba4ce9629317b9cf7bc8bb585dccfb7bdab56df9ede3c9754e34f5a383d0
test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb	644	4.86 KB	9c860d7f0069596b76c65856722937c5e39791e7142208572157a19928a0271d
test/data/soft/GSE3457_family_partial.soft	644	45.5 KB	dbb03aadc6b6db0a5a80b05b6b09ace4725fbdbd2862c6925d0a7c72b68aaef3
lib/bio/util/sirna.rb	644	7.33 KB	26edd6daebc70387f61effdc8aaf917f3c8c5c0ae9174bf24211857bb0b2221a
sample/dbget	644	1.17 KB	04ccde1383182e2490158b2c6b5fde219e2c9b15c46b4572a79e6d1844d6a7ea
lib/bio/shell/setup.rb	644	2.5 KB	8fe1225a57c89d14f61594b0cd2f6411bb3a33f90ce805780e19be7e3e349a25
test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq	644	984 Bytes	7f6e883493ac3be2114dfe4794e4a324bb67e7e9064c211bed60a6527c783b33
test/data/HMMER/hmmsearch.out	644	3.67 KB	575ce8e79d16903c9cf7670748e88bad399066ef5b9bb35f93cb36298d76b8f9
test/unit/bio/db/test_soft.rb	644	6.66 KB	b6bc93ea726026432fc0b909fefa7b488eca736cd703cc8a7ddc9ac9ab720c6f
lib/bio/alignment.rb	644	73.3 KB	bf467a8d5decdfe0bc8ac03ffb76b63766732457233da8da7a2fcefa71b23a22
lib/bio/appl/blast/wublast.rb	644	17.8 KB	1b5c7ffbe4c56e75a765c98f7b3d16ac5683be94ef5e56a8dad4ca8629ac5658
lib/bio/util/restriction_enzyme/range/cut_ranges.rb	644	1.21 KB	6367e63e557c219111df6e6d2006e7545db7d40082e7874a6bae643f870fc174
test/data/HMMER/hmmpfam.out	644	3.13 KB	e832f4b86eebeb3d956ca1ecef073986f108f22553916975a061b49d61c55c02
test/functional/bio/io/test_soapwsdl.rb	644	1.02 KB	92296789b65c198ae39579021244b682c81ae862fb8e0b3c65b95eb44940ccb8
test/unit/bio/io/test_flatfile.rb	644	5.91 KB	28724d6ceb6a934d7ba34797b8fceb3f22c128b8a0ea4be8f61bfd48cde60c8b
test/unit/bio/sequence/test_na.rb	644	6.67 KB	7c59e19845651317dbf495aa35e88507fb59b60d99360ada0ad090b54ef92c16
test/unit/bio/test_feature.rb	644	2.62 KB	1839b5b316f0729b6b6bfad29d90629e36ecbed7bc9c02da71ec4f68d51fb85e
test/unit/bio/test_reference.rb	644	5.56 KB	caca2529cdbeb49f04617f8113edc8987c0e1c6a4a413e2db5789dc2136ec431
test/unit/bio/sequence/test_aa.rb	644	2.5 KB	8353b7c5f2f96fbebebf12c8ad5d3cc13c4fe0b541fd2f1ac91881e7e73eea16
lib/bio/util/color_scheme/buried.rb	644	1.24 KB	9904524d8f999ef83de1568d72809c1999cece53397c655ef8776a78a38eafa9
sample/gb2fasta.rb	644	957 Bytes	9fe0f6c5c03d3fa500060f23208fb31d844ee810a36e5e4c6a73a784d736f796
bin/br_bioflat.rb	644	6.7 KB	a642f55f21661cd3be92051649d6e9ed1f5ff7a9ae1afb59d076c189844d6189
lib/bio/db/embl/uniprot.rb	644	951 Bytes	af4e716ecf160c6d3b1e48b8bdba8e449f388d0babc972a77f76d5294bea7d9a
lib/bio/db/genbank/ddbj.rb	644	423 Bytes	1e206a3f3f93eab293fd6533debae45d4c7575dfe1edda71f81f76846abcd036
lib/bio/db/kegg/taxonomy.rb	644	9.56 KB	2d0cc009d8c542c9207a70144e8250f7e3e755757eb6bfd8dd37d9cf69b79007
lib/bio/db/pdb/residue.rb	644	3.85 KB	1741ee45dfba640fdaa5bd50a5202d5827256aa0d4c05a97d0e9b1e739cf4649
lib/bio/io/ncbisoap.rb	644	3.87 KB	e95b248f5cb52e2cb4517d03961c439e4211dd77dbc6bf921dfd512e70d12978
lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif	644	1.4 KB	cb34983afbbf48685f0848c55692ed18b7fcfb20d92a7d65447bd9f75673ebbf
lib/bio/util/contingency_table.rb	644	11.6 KB	9c5b597106ea06c49113f888a7c1a0bf6730a5e916f41751aff98d5e560ae7fd
test/data/blast/b0002.faa.m7	644	5.52 KB	bb7d1c37f92f8a36527c02efb6f6352294eb1acf688ea6caedb7b934f9817e8f
test/unit/bio/appl/blast/test_xmlparser.rb	644	5.85 KB	fbd5285acc6ca8a8eff3702de99cd8f02bd7edf49202da1728541a3a26728be4
test/unit/bio/data/test_aa.rb	644	1.83 KB	93cda5232d62085aa4be1aa5727d00fa3acfba99bfe629aaf57369e5fadc6301
test/unit/bio/db/pdb/test_pdb.rb	644	3.34 KB	9b677d5119c65fb0aced828804b527cae400ec09ed9fcbf497a95645398e3a17
lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif	644	2.69 KB	0a62ede00f058222991d080db3b08ee22298ea956f4b666aa14c82fd747ab695
lib/bio/appl/blast/rexml.rb	644	3.99 KB	8da72461f6d6e5a65224b6c673631227493686fb6b9a1c2d7e48a8ef846e44f0
test/unit/bio/db/test_newick.rb	644	1.45 KB	308735dc5edd2a077059972e5d8431fd5ca5478df902ed883dc6bb2f1ff1da13
lib/bio/db/aaindex.rb	644	7.57 KB	ad6802a8be202fdb2479cd585af31a2e67c8cf30cad7f9c51d69a1128effa736
lib/bio/db/fasta.rb	644	25.9 KB	bd949fdc0ff6e87d686f7b3d80fd8474dcaf724fef6475e3e3012d238a672517
test/data/prosite/prosite.dat	644	167 KB	cffe5a81263ac7e3877bab8f7d32e27ea722411b4d4f0fca235fe4e552fae671
test/unit/bio/appl/tmhmm/test_report.rb	644	3.28 KB	cc4e1f6ac3f9ccc21e764d103f840101790321e8b5d6c8d18cbf16b772fdeb41
lib/bio/db/rebase.rb	644	13.8 KB	5b77f101bcb6383037a0e8a2262e34a4b4ab984f6c6ad47e90ccc38d20ed0630
lib/bio/appl/phylip/distance_matrix.rb	644	2.63 KB	24455644af9afe549c082972df362c5caa3d3eea3db29b2298f975a05d3c6626
lib/bio/appl/psort.rb	644	14.9 KB	76967a5fa6ae16c3ec881f43072d4561b121fced1ce9e6d062058b9a1031a4e3
lib/bio/appl/spidey/report.rb	644	19 KB	e7ec75fc26c812cc81deaa8653dfba4418ce4910a4ae63cc6dc6e938673b17df
lib/bio/db/embl/sptr.rb	644	34.9 KB	2179e53a677f5908460c9083f379670c26b2e1e79866f4f74ed2a703c76a6a5d
lib/bio/db/fantom.rb	644	15.1 KB	16ed579f0444447fa1468b19ac4f0a3f4c2dfab2b70b769f8d0919a374777515
lib/bio/db/kegg/drug.rb	644	1.26 KB	fe194e0a087fbbcb2fa1d09f753ab18ab320c79f026078edc6ad9182893c6572
lib/bio/db/kegg/enzyme.rb	644	2.08 KB	8c363a1ffd318eb569b062dbdcea778a48182f281d66420651ba410622a6fabf
lib/bio/db/kegg/expression.rb	644	2.98 KB	8f4213871035a65826092c39a47a5f0302e57fe9a9e296f056faf76c3027023d
lib/bio/db/lasergene.rb	644	8.87 KB	6be38b378abd5dd0a73211a9a18125dd6b91588acf85d9b62dc9fe4f0ce5a0eb
lib/bio/db/pdb.rb	644	594 Bytes	75fb017faf8c188ceb846336c581b5455cffe63c4cc6ff6d3e26e264a1d3325c
lib/bio/db/transfac.rb	644	5.89 KB	9517ff987b3420e897fdc690f233ceb3cd9734257ecb33a2b4ebd9fb2d3a1008
lib/bio/io/ensembl.rb	644	5.74 KB	1b164463566711c738fad223b26f672d0552cea2ef0352cb375f4ac4e02ad45e
lib/bio/io/fastacmd.rb	644	4.1 KB	fbbc315bd926712bf1e78e5acbb31beac08f4550fe05277a6bece94db822e2c8
lib/bio/location.rb	644	25 KB	1d94ba954fc0544f42062a62acd7a9390bf91645e63c5614effe9bd010f55426
lib/bio/sequence.rb	644	14.9 KB	6c1efc14561d0c05076a9d060e7773be057ad22f448614e3ce17f9a46adcf4f4
lib/bio/shell/plugin/das.rb	644	1.01 KB	65258848a7b0c1e90740cdfd8235c478c92ac1a434b19255c38abd2544abed05
lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb	644	1.44 KB	fc5a1c4a457ee8916fdcf47eeedbf937f52ac7aa9c8da9c6b62e75778c870005
lib/bio/util/color_scheme/taylor.rb	644	1.07 KB	1af407d819e588fd266b4076e08849c3f7fe6211cd9799b8db2126286ee5e17e
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb	644	2.9 KB	1fcd5f98ac571a6af6a1a13c4d74dc9eddd524454edd2d5b1c7f98ab858c4ae8
lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb	644	949 Bytes	d9f9349d45f95f3e753b7b8650da42e032ac0bc3db6a8c5db0d4ec9b4c7a8573
sample/biofetch.rb	644	12.2 KB	0e2e2a35cc2970bf0cefaa6d4befb431082a0391228435cb9f15df3ded3970c9
test/unit/bio/appl/sosui/test_report.rb	644	1.82 KB	12c0ae343b75ea99666feae1c4b40eac8e363043109c510bb35e511c60700f0d
test/unit/bio/appl/targetp/test_report.rb	644	3.7 KB	05fbbbe11fb46ed996cb87f20846ee3c12aa08d846915f549e43699702fefc20
test/unit/bio/data/test_na.rb	644	1.81 KB	2a43af919f53aa04750973cb41e7a05588f9cd0c0c1fe80a91936f1f68d80fd3
test/unit/bio/db/test_nexus.rb	644	15.7 KB	123e6d9169761d716cfab67c410377564e69b1d4e943ac4a7a92bf367c8d4b91
test/unit/bio/db/test_rebase.rb	644	2.48 KB	133e2276b79c1b047da8040b1d586ec368fa276255488d9c0fe846a18f5f5cc5
bin/br_biogetseq.rb	644	799 Bytes	2ceea85a863d416213b4d4e1aebdb53cfbf3a6fd84fdb9f36c7a50a85bb32a60
bin/br_pmfetch.rb	644	9.93 KB	32e4f61ffa9fea3ca79329241da004f5d81ffd7379cee7b3e5fa0d4b34649e46
lib/bio/appl/emboss.rb	644	4.41 KB	8ecfd9e3bd178a58b0a6180defda08dcf5365400a7c0d7dee5343afaecb811ad
lib/bio/appl/fasta.rb	644	6.3 KB	b87f74a13e7de0b9e6da1e8fe39d6b79ff4b952f77f084ee9226b471f2c66678
lib/bio/db/embl/embl.rb	644	8.84 KB	bf1fe941b747183395e4a68a33a88d80d24a9ebe7e39455eea19b64068c5ddc9
lib/bio/io/flatfile/indexer.rb	644	26.1 KB	c5ce43379a5e74cc0d1b451fb504c8e0b79373f262c74fdd91db26b5070fc469
lib/bio/io/flatfile.rb	644	37.4 KB	b6171747cd2c0640618954c01be825b6dbc3803f3318a11b96d472af7eed7728
test/unit/bio/db/test_fasta.rb	644	8.47 KB	6377df17d2105774bc5e817fdd66c84cb7e8a9f8f0499d9b9475e181a3f7534e
test/unit/bio/db/test_prosite.rb	644	18 KB	b86ceea50a7e585cc2ba2cb9f442844e8834e0117b048a57a90a6f7ab76201f6
test/unit/bio/test_command.rb	644	8.39 KB	85b0e18a4e972adf1b9cad12c2d3543c1f33c9715b2f7bce59b00561be37b10f
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb	644	1.43 KB	06bf4e6e0293a2daa3240467398e83b7ca291f7a33138fb45211fbdcf80c1682
test/unit/bio/util/test_restriction_enzyme.rb	644	1.12 KB	6c4d73ea2c0f858940273a8d36e60586ab69a9c56cf2041780268fb4e1fb060c
doc/Tutorial.rd.ja	644	82.3 KB	3f3ab5e9eb34a40d237518a4834963e72665c9d798861e243b2024c61f71f5ef
lib/bio/appl/blast/format8.rb	644	1.9 KB	4eecfb1e3e153ba96c6a594a2561c31c5280a188c3780b79aa848955eb6e1487
test/unit/bio/util/restriction_enzyme/test_single_strand.rb	644	4.8 KB	bece1acf19415b276ea5e80e0f943d61cac72a91f0cea36d3a87dff0e51bf30a
lib/bio/appl/blast/format0.rb	644	49.2 KB	72c122c2941774ef0d5a25cccb3ec3780ee1e10c6f6c9fe3ff1039749ae3fb63
lib/bio/appl/blast.rb	644	9.58 KB	cbf7e2fd75a40fc4366c472de724af26c4450063899afaa6b187044e25caf3ec
lib/bio/db/embl/trembl.rb	644	1010 Bytes	75b1c109bfff4503e62e67c940d16231d736ec49e604dcffa43c009444f19477
lib/bio/db/genbank/genbank.rb	644	4.47 KB	3e3569f4597ca5fc39542dedcf65a482f1c98c12e2717cd25feb34e228f9adff
lib/bio/util/color_scheme.rb	644	5 KB	e143c2d3e5f9115ff4e9a5806c1ea8cd4f50745e21529effa1d36f729b33baa3
lib/bio/util/restriction_enzyme.rb	644	7.96 KB	afd9d77484d5d21043ad573c87004e42678fc6d8e999fa452a509342602d156c
test/unit/bio/db/kegg/test_genes.rb	644	1.08 KB	d54b0dcfafea74a46e6fc6076aeb53c8b05f08ff11abbe1e2a68ea5f48d1941c
lib/bio/appl/sim4.rb	644	3.3 KB	0738d0d14c2f1ec99a5125831ae2ee3c3de5f09ce6489ee50e9eb82e7d5f2662
lib/bio/db/nbrf.rb	644	5.2 KB	662f0b5ac3817bdaee7822faa93d325fc268dddfebcc821a2c240fc1a68b9f17
lib/bio/io/ddbjxml.rb	644	14.1 KB	833505c296409629d5e2cd57aab438cce9a326687df13cf8540a84cf47580c8e
test/unit/bio/db/test_gff.rb	644	3.41 KB	df91df52aeef6e32969c605fb90e8402811437cb5773e564f700057b7bbc1ddd
lib/bio/appl/blast/xmlparser.rb	644	6.36 KB	913a62bea89c203a24315579db9be0bc4274baba6c88a7dbac28b3cb0ae5d752
lib/bio/appl/probcons.rb	644	1.16 KB	f8899e8ac6e99ecf62a793507c2e51c4be2fb3a69f0c44e02bec869a9e3fb867
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