bio-2.0.3

https://rubygems.org

bio

quick gemspec

.gem

.gem metadata (gemspec)

.gemspec

id: 11299

number: 2.0.3

platform: ruby

spec_sha256: 916fc4df916e3f2cbdedc67a26dfb4a6ba834939ddbd6da1cc68db7a32a00149

sha256: b931ed0c94498bacb8c7dbd87c680672dbbae059299a3be1ee8c9f2b56b5816f

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

updated_at: 2024-05-23 19:20:26 UTC

position: 2

version_data_entries_count: 564

uploaded_at: 2021-11-05 20:07:51 UTC

indexed: true

has_extensions:

extensions:

Gem size: 1.29 MB

Version Data Entries

Total: 564

Unpacked size: 5.19 MB

Full NameModeUIDGIDMtimeLinknameSizeSHA
appveyor.yml10064400647 Bytes16704219d80ff425fb44059a1e33494e0941e5c4cbee43efc92a9b238d755bb3
test/data/blast/b0002.faa.m0100644005.15 KB2479b6f0b728c354edbf01fe600cd7884308e1e6a22913a7420e23af75cbfd75
test/data/blast/b0002.faa.m7100644005.52 KBbb7d1c37f92f8a36527c02efb6f6352294eb1acf688ea6caedb7b934f9817e8f
COPYING100644002.45 KB5aa669eff3739ec0aed66dd1b5fbbd30cdcc4187616996c33fd21634f518a4ad
LEGAL100644004.2 KB9a330b8b5a2d2272adac16e19727fba25cd5e0249a641be60cfb96103375b9ea
COPYING.ja100644002.56 KBd39fd6ed81dca7c84929f74c365b9f21329c5ddd41c8cef52f9f5ca76801dea1
LGPL1006440025.8 KBa190dc9c8043755d90f8b0a75fa66b9e42d4af4c980bf5ddc633f0124db3cee7
lib/bio/appl/blast/genomenet.rb100644009.09 KBf0574c89ea4b90c8ba18e816ddf51eacf4910c8a1fd2e372b6f8967a14f8fea2
lib/bio/appl/gcg/msf.rb100644005.11 KBc7c41a817f780d45c126c42e4fa1e78ebb986e9e0596f103f4627001ec73585f
lib/bio/compat/features.rb100644004.5 KB8a247d12e629ed46fc4e7f11f632b8e7f9cfae9b98a8af18e3a7c2d999d815a6
lib/bio/db/embl/uniprot.rb10064400640 Bytesbfb2a60218b048128f33bbaba9539a5c5b0b76851d9b1bd9281b9e32c8c5ff54
lib/bio/db/genbank/refseq.rb10064400533 Bytese45d2dc1df5df3693183c8786bb346884cdf99580ae14adeca9ba7c23219aacc
lib/bio/db/kegg/kgml.rb1006440016.8 KBff14c6e4c22e27045063e4acf774132c2918a744bc0bda756a32738b4dc8fb65
lib/bio/db/pdb/pdb.rb1006440062.6 KB85f304bfec4ad37dee66aea4c9cfd3035e84118c287291df253f18b5f9161793
lib/bio/db/prosite.rb1006440011 KB827588b748f43c7dabc13662d2f97cc3460bf41963bb86912bcf56e55c1dd6d9
lib/bio/io/flatfile/buffer.rb100644008.26 KB4e9bd37ac8435140de2b12aab6b00ac09da442d59315d55af26f0e4b4b491e00
lib/bio/sequence/dblink.rb100644001.27 KB7b7700570bfd70021b052ab7b62c95ff2313c1c39a181387d101f56e31446c58
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb100644001007 Bytes5281b2833ece6cae6cd3ddcafa38e261a4b427f3cb6909903459e40a3cbfec88
sample/biofetch.rb1007550013.8 KBe4a653f11d59932b205f3f3b29847589bb647b49808d442a564cbd20a9cd83c3
sample/demo_kegg_orthology.rb100644001.3 KBc6016b1bad4fed0612152aee694b32755412fec276a9cb157e2626519f97f4f1
sample/genes2pep.rb10075500955 Bytesc8e66040931bfaf471485d02057b6f1efb407805045541cd7152ada2bc11860a
sample/goslim.rb100755006.62 KBf88251ccd40a5548b5b1fa9e6515732282f53a3819185afb67b78b4b69991f14
sample/na2aa.rb10075500413 Bytesa2f121a4bc0a5732b9620771f3c2550e0e57fbb648451b952466e41001a93dfb
sample/seqdatabase.ini100644003.41 KB0a930f4502c1dc0ca6adf2ec50c2bda9e8b213d618edb2532017e9443ab58d9a
test/data/KEGG/G00024.glycan100644002.32 KB203ec01248d66a18e40a046c9f30c0a4bcd2a124cdd40599a29c785280c78c2e
test/data/KEGG/b0529.gene100644002.52 KBfaa9f0534c9b79d8632ac5b0558371a67b97bbea47d96d170e81373038f5e12e
test/data/fastq/illumina_full_range_as_sanger.fastq10064400426 Bytes4148a8f6ae111de3d10933e1055dadb932e6f93926f75cf3983d36646fe37e90
test/data/genbank/SCU49845.gb1006440010.2 KBe9a1e1626188afc7168680a9c0039be85f1298f140165d6cb67c707b0b6fd660
test/data/rpsblast/misc.rpsblast100644007.26 KB9e44883a6a78e25db6da697431f3d64a6844cc4fd05d39e2bc2eca7b4cf428c4
test/data/uniprot/p53_human.uniprot1006440071 KBcf6237bed4c283ab5a40c330c6554d49a1ab52f48069cfd90f3082edfde2ea98
test/unit/bio/appl/bl2seq/test_report.rb100644003.5 KB3b49a9258d80356d8639eefea711ded3ab302bcac8025bb544bba3e70758e9da
test/unit/bio/appl/gcg/test_msf.rb100644004.45 KB88a50ea29fc6c3eccea1c97eb35ef75bf79e68d2646b15b99fb1f3e0df50972a
test/unit/bio/db/kegg/test_orthology.rb100644005.42 KBd365425ed88ae8871297972a9169c7754a17125f73e829cc547ba75875d05283
test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb1006440010.2 KBb81fe69319e35852270f6bf71d7a15478c7db84bc7d77d210f8b49bfe8dbb92d
test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb100644005.01 KBfd06c157fb3651742ec58924ddde7d69744eebcbab4c3034a70d8a521359cf54
test/data/fastq/error_qual_unit_sep.fastq10064400608 Bytesa819e7f2a4d33695eb1916112d4ca95ab16bd58f7fcf1ef4798d854b59ceeae3
lib/bio/util/restriction_enzyme.rb100644008.08 KBe7d7674fd1219b879129c62fb1f89e84943167572961c11238e7a8e6e2ec8137
lib/bio/db/medline.rb100644007.44 KB4c78a0c7db33b0b7ccedc9fc6b3446c1edd8bef9686b1422d71c63c3b59dd454
test/unit/bio/appl/meme/mast/test_report.rb100644001.15 KB33e2f7b746315e46468e66a0e59bf83f323eca9cc935a4c85a146f00a3d4b0b3
lib/bio/appl/blast/rpsblast.rb100644008.89 KB6c97aada2f57163ec5f366af4e9b40c85db3ca542d70940c19dcae254397cea8
test/unit/bio/db/kegg/test_genome.rb1006440013.9 KB4361603279699cf45699702afa05ddc2dce7083a31c51afe3881df8f36afd5b8
test/unit/bio/db/sanger_chromatogram/test_scf.rb100644004.46 KBfed24db3a7a2fdc7dc0f14bc5beb28b1c418fabac7e76d8bc6026a7c90f11c23
lib/bio/appl/spidey/report.rb1006440019 KBe7ec75fc26c812cc81deaa8653dfba4418ce4910a4ae63cc6dc6e938673b17df
test/unit/bio/appl/genscan/test_report.rb100644004.84 KB62107663287c7a4d74b63b64f1ee1d85d9269b4caf5ed27efd32dcd209050b22
test/unit/bio/db/test_soft.rb100644006.58 KB08a0cd71551b0c03667ef21988b94e31aade89384eb601e4e9f5f0c3897599d8
test/data/fastq/sanger_full_range_as_solexa.fastq10064400550 Bytesa7ce416a53df877a08592025830be338b345330c61064ce2499532f6a2497d40
doc/RELEASE_NOTES-1.5.0.rdoc100644009.9 KB95b843108bec03de71ff421f942f1d46eaf71269d25b5099f25a70820b16057a
gemfiles/Gemfile.travis-jruby1.810064400111 Bytes0f7a91764dc9e0183471b039378b1d73c6895044d0a1039e6654066c42c2fad2
lib/bio/appl/iprscan/report.rb1006440011.7 KB4866e2cd674b0f5f62443c0ff7ec7d945cf50e24eb5651d17f6dc7707c36f573
lib/bio/appl/meme/motif.rb100644001.04 KB7176b41894d500bb58fb39b86ba1e71601b5d8edb4f0054347c6a529ae6e8e19
lib/bio/appl/paml/yn00.rb100644002.79 KB17fc612d7db16c1035adc7979da1d611a667210fb0a6bc94f50e7b6b600649cb
lib/bio/db/embl/sptr.rb10064400552 Bytese79684fdfa252015db904b6d2c71e964a3f76cd9c2e543b81b8e76e3fcafac24
lib/bio/db/fantom.rb1006440015.1 KBdf4cb4028ff7f360313e1ba638968c6c55ac99890a10bf76fc759a0076ee46ee
lib/bio/db/fasta/format_fasta.rb100644002.81 KB0bc7e51d2aa1221d5b77f42afd553bdcf5bb5eccd39a16a8d80faa28f5a0d89a
lib/bio/db/genbank/genbank.rb100644004.09 KB882fb7d27ca272b81e2853139510a58c41ac3ad44ae497790dbd8caa751590d1
lib/bio/db/genbank/genpept.rb100644001.22 KB8317e99c04999c216d5234034ecbfad0c679ca42d5e8793aab551fc8cfba2f7b
lib/bio/db/kegg/genes.rb100644009.98 KB83f6177bdedd2ff8bd8ab65087a42245fdf48b7b0d339f5b100cc65a3c4e8e82
lib/bio/db/kegg/module.rb100644003.55 KB70b6356ec28b45c313dbea40b5d65e65c6f8b3d5441e60805adddbb887843eba
lib/bio/db/lasergene.rb100644008.81 KBab810df2b17490d5b9e55de9e96999ccb14ca3d2e8bb19614a8ff34f169d1f44
lib/bio/io/hinv.rb1006440011.5 KB3e5db0084c89f0846dc9ff93f7137e7fea67a5ede5feb91377e131fdd0582fd8
lib/bio/io/togows.rb1006440014.2 KBe4abfb7aee2e5262e28c2a42344baa8abe7d9c109568ac4e4d6b4dddf3705d62
lib/bio/util/color_scheme/strand.rb100644001.25 KB875060462cd79b26800c6a6122c21083fc55747ed85325162db2ac21038a18b1
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb100644002.88 KB9d849388f0f6691ab87d3fdfe1e6d55698df79049b93bc09972d4bf98bfdded6
lib/bio/util/restriction_enzyme/string_formatting.rb100644002.8 KB20825b401ea6644b78825f1dcedda3872eb163f1feb71bf37400baaf13403c0b
sample/demo_codontable.rb100644002.84 KB0c63856ae537ef03835eac5827efacfc9f3f26c85928f2e89cbbe8189dad048a
sample/demo_fastaformat.rb100644002.43 KBe5522eca1e7c5fdb2c853df473ef6f1c607bd65ee646cd8bcd8648af5f03dcd3
sample/demo_kegg_drug.rb100644001.27 KB6852a6cccce5590fae8c7963961eccde179204ad461dc350be5256f147612264
sample/demo_nucleicacid.rb10064400954 Bytes5d0374ea992c87e9c08d3dc63629ec5a2aa3f6fa2610cdd08f5b288f18418591
sample/demo_tmhmm_report.rb100644001.36 KBa6517a2b8fac40759b81953333a3309cf1b89aaae0fe31a194c021947ed965bf
sample/genome2rb.rb10075500910 Bytesc163eac8c0477dd2b7f93400518da3f656d11de834693f82c432add97876cb06
sample/pmsearch.rb100755001.32 KB485c955f5493b3056e13c335572cde72f9f676ae80a2a70b06b7f22a3d1e3422
test/data/KEGG/ec00072.pathway10064400870 Bytes2f97e02e90e5684847dbd2363dd8f452e912c5ef319f5d74085468e274b7a92b
test/data/blast/2.2.15.blastp.m71006440067.2 KB723f8d684b11de6b01630896e6e96b37d95dc80344bf550128bf27b59200cb8b
test/data/fasta/example1.txt100644004.66 KB7b441d36bd74e2bb8662c58aee4fd9003efe79a59eb0449558f4855d839c3bf8
test/data/fastq/error_qual_tab.fastq10064400609 Bytesc2a85269fc0b2f6b0b8dc02d6026b583b82638fcc8e76f2888bbcef1da57f015
test/data/fastq/misc_dna_as_solexa.fastq10064400767 Bytes5323e24d25cf1ca763dd002553a80424c4e4e2011bd677eb60ba05ea3d7c410d
test/data/sim4/simple2-A4.sim410064400672 Bytesdce2c8000b726b2ead80fae52e4765da3572e174534e691e919d38d9787fd301
test/unit/bio/appl/mafft/test_report.rb100644001.97 KB714147bf14490dd7197cf4596afbdb4d22922bb2d517ed6232e7e4a0fc399cd1
test/unit/bio/db/embl/test_uniprotkb.rb1006440080.5 KB3c3eb789c6459be478ef420df790877a11d7f5e841d7857b0b444252ff07847f
test/unit/bio/db/embl/test_uniprotkb_new_part.rb100644005.81 KB705634dca06199c0541becb2b6b847ee0518f0bfc9648eb525fa1f288eded5c4
test/unit/bio/db/fasta/test_format_qual.rb1006440012.3 KBb4cbaf41abba7674ef51a9f804edb2ea74d1783a09bf292d9831a3c6273e5a2b
test/unit/bio/db/test_newick.rb100644009.92 KB825a44b21570a540114e637260b1cf3559b3cd61d19fec00e613d6fb387a128a
sample/fasta2tab.rb100755002.33 KBec5e4a2ee4cc4f219cb2274886beecb8485edc60b6d8c04e8c3a4f4324455028
gemfiles/Gemfile.travis-jruby1.91006440054 Bytese29b47b5105bdb7120803e781d1a7df235678b9abec0d298a2286feacd6699df
lib/bio/appl/muscle.rb100644001.37 KB3913777ac7be3249cd810bc9718b5cad5c33f1baf8b81f86176551db71436bc5
lib/bio/db/nexus.rb1006440054.9 KBd6685252ee11c93c5e4455c865e00d5b8ca5792699c46c257864d7219f53dc16
lib/bio/db/soft.rb1006440013.9 KB8aaa8b3bbab6b26c0b8a80f6361f42422208b83b6da3142dd6106950d3297ccc
test/unit/bio/appl/paml/codeml/test_report.rb100644007.06 KB2778e99bc756aadb5867dc5c4a9d71264224fda2764cf6aac2fdcd1545f60301
test/unit/bio/db/pdb/test_pdb.rb10064400100 KB1d3dfb382a1cfde7affc1dbf2c6924a419e54a7e7531c56f9c99881f3a1139d8
test/unit/bio/util/restriction_enzyme/test_double_stranded.rb100644003.83 KB8e71d644dac4188ac4e3a6a850af252febfafcff1f0c2e627865369033729424
test/unit/bio/db/fasta/test_defline_misc.rb1006440012.4 KB38b06490a9798a2fd4deb4fcf800940c4656556cf0fca68087e916a5ca17e434
gemfiles/Gemfile.travis-ruby1.91006440054 Bytese29b47b5105bdb7120803e781d1a7df235678b9abec0d298a2286feacd6699df
lib/bio.rb100644008.27 KB41622d9a93822620efd8bbe7f39ca73500bbed75680ec1844955e9edaddf5000
lib/bio/appl/blast/format0.rb1006440043.9 KBbdaa706ea5bfc501145f36c6f6c67c5a91b981cd458764d9290bbfd78e853b89
lib/bio/appl/clustalw.rb100644005.98 KB1e51eff966b274cec63a5d10e2ac61cb598b9125163c63ac4b9a443b23c1d1d5
lib/bio/appl/clustalw/report.rb100644005.1 KB30a3b023e43bb20b100ba34a48afc390a3e0c48f66ed71689c3361ac28c7b4d2
lib/bio/appl/fasta/format10.rb100644008.86 KB9bf77b83abc82ab68e6c1f61092a6816b2356bf6aec6018dbd36f401dbb46e7a
lib/bio/appl/paml/baseml.rb100644002.74 KB57e1ba4b3a8b914c9165e6ac4c99e9c8d3229bc6bab99c4befc99e0fbe4c8808
lib/bio/appl/phylip/alignment.rb100644003.36 KB74ab9a941fc46def4555c416d5502eaf884d8fe7da4499b14a57df98c5d15ec2
lib/bio/data/codontable.rb1006440060 KB46669654ec3aaabc3ee528abea9e34b869d2046f8d199f1919b12203236d4b8c
lib/bio/db/fasta/qual_to_biosequence.rb10064400758 Bytes7f3997bde56110f67c646884ace71637ef925f58a3fa4edf625aefe6e165a7ce
lib/bio/db/gff.rb1006440060.2 KB864721fa37b67c23c74d7e088e9c0c40b475ee22a1f4bd436953489520410e29
lib/bio/db/kegg/compound.rb100644002.51 KB202f1eeaa6715d177c7089c13d30d12eb8edab28a3a8e21f05d66652b07f7e95
lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb100644001.75 KBe03d803b8352255ec227013a1639d0a9e8511ddfbbf11939e82984ee7f208382
lib/bio/util/restriction_enzyme/single_strand.rb100644006.65 KBc3ff0739c9bf6e94d07e8073c7ef8529232ab1d63287cfe1d36ea881b874e997
sample/demo_blast_report.rb1006440010.1 KBaf533f7e723ee515ebfd88e973bd52efb89dc883b365a9606656c9c9ceb3f162
sample/demo_genbank.rb100644002.48 KB7093bd7cd51c642086901daafac00db41bc63c44947a5fe7ed4aeb72cde63e4f
sample/demo_sequence.rb100644004.24 KB61b81c325020c522e771fa6229a45c0ea3e82ab1bdc9e019e45848e7a548819f
test/data/HMMER/hmmpfam.out100644003.13 KBe832f4b86eebeb3d956ca1ecef073986f108f22553916975a061b49d61c55c02
test/data/KEGG/G01366.glycan10064400545 Bytese103e8ecab1b285dd603215f6ce8a30e8fc7ca3f625c01967b7c5a4029bd42c7
test/data/KEGG/hsa00790.pathway100644003.05 KB6ca9a6e9170fee93de9269641f4aa9c416cb3b5122761810af94707600d4613f
test/data/KEGG/rn00250.pathway100644006.12 KBe684bcf769a8da079baa4ae3090d2d711a9db50322965464aabc0982af2b23d7
test/data/SOSUI/sample.report10064400414 Bytes1925c1a9a14b535fcdbc76c4e57ac1195a9f830c63345423ee426def973aa333
test/data/bl2seq/cd8a_cd8b_blastp.bl2seq100644001.54 KBbacf6a696044c0751edd37d72025326ac19417e39f76139e1ac568d54c098e2f
test/data/embl/AB090716.embl100644002.47 KB0cf0a12b44f6472a021abcf4dc38f2f8a64d6dd4049463056057968e2ce0f0f4
test/data/fastq/README.txt100644004.83 KBaca3f26a1c8d8bab7dca1e1cf8ba73d14d3ae34575f8d348b2ab5eb4d365d5d8
test/data/fastq/longreads_as_illumina.fastq100644008.19 KB3be788dd8a50564cb7b2bdddd3005c41dc85ec866242f8979d1223b97f370447
test/data/fastq/misc_rna_as_solexa.fastq10064400774 Bytes073dd9509de2be068bae20cae68c546727c8043de53298a3093afbffa9dda3f2
test/data/fastq/wrapping_as_solexa.fastq10064400963 Bytes73211e22ce6ce16d579f3ee1a2dc0eec913e20799185655305bbbd7670364811
test/data/iprscan/merged.txt100644005.17 KBb8920e4a017e8c9d0bdd837bf6691c8ed13fe3dfad8f5992b97cdb1f4db62b8c
test/data/meme/mast100644000 Bytese3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
test/unit/bio/db/fasta/test_defline.rb100644007.77 KBe28017019d7bfc8e06647d624384b5ac88568702792a2905b7439be0d122ec74
test/unit/bio/io/flatfile/test_buffer.rb1006440011.5 KB3e506a0f0c3b9d220e6779be834bb58240c6a8b420550fbffeefe65abe503269
test/unit/bio/sequence/test_ruby3.rb1006440012 KB1c694fc6817914a2925f70099e3e2e9373eab7459d35b5f949e483d6e80e6b59
test/unit/bio/test_reference.rb100644008.12 KBb9fc2aa5a9f8d6e18967bc1d2d12ed451ea82e56f9b3102be7344b395048ed6c
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb100644002.2 KBdd35fc665ed061594953f2a98495febde2b1cf9a53c927a096d94af1c2b96f68
test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb100644001.31 KB900639ed4e1a581307b1dbdc126698024af756cf71b2077fdfea4542a47e7071
test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb100644007.28 KBcef1260b9a0e4667015d3ef88d3b45a64126db5c20239f72874515d7b288a591
lib/bio/appl/hmmer.rb100644002.07 KB1e017eb253ba728e6f46226e8e4720da003a8fe6b994c51ccd506913c50bf9d3
test/data/fastq/error_short_qual.fastq10064400607 Bytesf92205c3a8e15c4cb233fd3de4876f2ef0d34ab5693db30a9da6149bcdebe0dd
lib/bio/appl/paml/baseml/report.rb10064400660 Bytes9a4c272ea61596c13451459b6dcf3b386a3149ca20f972bd1b2ac0177ab82734
lib/bio/io/flatfile/bdb.rb100644005.55 KBa0151a2360d3e2a0604e37b78830c26c9da2f84a29d89015476e35a525a7d26e
lib/bio/sequence/aa.rb100644003.08 KBd8863eb071dbfb524f9a0c2cf9608ad0020455f86d6ee8fe01808c62948103f5
lib/bio/sequence/adapter.rb100644003.7 KB40e2012097a720593ac504c1c63a65e11b2f0f306ad51dbac4b74ec5457cc447
test/data/blast/blastp-multi.m71006440011 KBc99e14d4bcb868f03515051dd8c0c32da98f580e22b9212425b6c775d6b8fa06
test/unit/bio/db/kegg/test_drug.rb100644006 KB7f6996d9f6ba6d2b1df27d5e0a32d3c3363533bbdec344b2903bb726be41ddee
.travis.yml100644001.82 KB1752a796d7b158044693255c88a564813083d3c5ebfc48049e0a6d9002051713
ChangeLog1006440051.6 KB8568025153d0d833560adcb1c7112646dfd3c420f3ae1de0c4c9155541d62ec5
gemfiles/prepare-gemspec.rb10064400615 Bytes9960cd28c2d5747e2e6bc024a2ebd81e7a8e19a7d2b0ce0bbcb46e259520d5d4
sample/demo_kegg_glycan.rb100644001.5 KB7716f364760283313fcd39d9b86f34ba6dafed0799855657cc834982b3316f32
lib/bio/appl/blast/ncbioptions.rb100644005.51 KB345225a780c91d01ce15b07a5458aeb369f738c8ebf1de765ab1bc07e83d60e1
lib/bio/appl/blast/remote.rb100644002.73 KB5093479f426cf7c15af84e89d4c3fcf58caa8fe038c74d3e43511cc77eb126f6
lib/bio/appl/paml/codeml.rb100644008.11 KBc2bf12cf6488e7d2f3d6f10c8cf762f4865c8bdf8f2630d9aabb7374f2336143
lib/bio/db/fastq.rb1006440018.1 KB92762f36a334a7c1c9d01135b7e81f51761adf643c5dc0823a3dd89dec9ce99c
lib/bio/db/go.rb100644009.8 KB7a99bab65b50eb4b43b1426002c523a4ec6c610529495caee9c0f4771ba7eac1
lib/bio/db/kegg/reaction.rb100644003.13 KBa38f78c0a6899e764513b6bc09476e2791dd58b318c41619590bfe9f87c3be0d
lib/bio/db/nbrf.rb100644005.2 KB662f0b5ac3817bdaee7822faa93d325fc268dddfebcc821a2c240fc1a68b9f17
lib/bio/db/newick.rb1006440011.9 KBc51eb3204d1c8d0fbc32b6268e98f7ab9a1481951d28949aa530fdf80ec4ff56
lib/bio/db/pdb/chemicalcomponent.rb100644006.64 KB56041809309243d1aafd10f495ff2d0de4287e9920ff140e9be752be06da7d56
lib/bio/util/color_scheme/helix.rb100644001.25 KB565b1a9f94431205873436ba4a2ab2a3e3267c9bf3e0cce246ef661c49109ef7
lib/bio/util/color_scheme/turn.rb100644001.24 KBbd3eccff3a257ba853884956d26e8da73b68412375bf9531af7964a991ced74e
lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb100644003.14 KB146790c0b04376c7da456928908f66f356858e146bc869006992120686cbf0f1
lib/bio/util/restriction_enzyme/enzymes.yaml1006440087.5 KB56ed1fd2f2d5557604da2044f3d491ccc5b845c43b4b307b395fb89e3798b346
lib/bio/util/restriction_enzyme/single_strand_complement.rb10064400701 Bytesd902cedac2129460a1fdd3408cd8bdb8314d72f051aeca1da93c34ffd5892b4b
sample/fastq2html.rb100644002.07 KB82986b8acac90a3025b6ed57da1b86893380c06b9154e665b8c53b5205df2911
sample/rev_comp.testdata.yaml10064400196 Bytes3e5a8971a14eb4d312b6b1b2d2e42f3806e7f50f618024af3f58829e28326a2c
sample/test_restriction_enzyme_long.rb10064400204 KB32fc46d7a6531aefbb1696295f36826c4c82443f15ca66f900ee3671a6b366cc
test/data/KEGG/1.1.1.1.enzyme1006440042 KB3abaef4380391a3bde08232e79074e336d1d29d78f3c8185f8b1dc11e7790226
test/data/KEGG/D00063.drug100644003.92 KBd7941a74bd701f93ab057f6e4ab21cd043d7e53c4885a85be8d352f7329df3d8
test/data/KEGG/map00052.pathway10064400774 Bytes584214ffb5c8e27918856f82d2cf1c77986ff8ab1d9062f9bc1492f93d00ef44
test/data/KEGG/test.kgml100644001.7 KB5626abada68ac5bc6dce2da889970ba8d24fcc91050e59b4ee79d7eeaecdb3ae
test/data/command/echoarg2.bat100755008 Bytese4647efd47d7ad4edca4f3725a4f9610157cbc8fd9023666c3183400120b2358
test/data/command/echoarg2.sh1007550027 Bytes8899571341d86d26900d235b234fe156034d4177a8dca172cebac099cf05391e
test/data/fastq/error_tabs.fastq10064400629 Bytesbcf82ae47fca310a4ab418438f6158d47e9e93d5a4b8d0258230c58f15674301
test/data/fastq/misc_dna_as_sanger.fastq10064400767 Bytes56d7fb3045c6f0ef3e2a4e35c4e4ccca79674c4a561e4e5f70a164e0d2393f51
test/data/fastq/misc_dna_original_sanger.fastq10064400767 Bytes56d7fb3045c6f0ef3e2a4e35c4e4ccca79674c4a561e4e5f70a164e0d2393f51
test/data/fastq/misc_rna_original_sanger.fastq10064400774 Bytesb50686397fc812ecf7c726901acc1f127be1d29dcb6039bf35970e378ba51893
test/data/paml/codeml/models/alignment.phy100644002.48 KB9441a5ba369293ab4cdb5cf722f920ade20176d996a9d24278803c4c50890e15
test/data/paml/codeml/models/results7-8.txt1006440021.4 KB37d4a57c457c55ac5e09b585c7020cdbb79a765833e85b41674c26aea9032f01
test/unit/bio/db/kegg/test_kgml.rb1006440026 KBe887f4f2c3ed1baf429e1625bd7ae46de08562f4e717df5fc281262391973184
test/unit/bio/db/test_fasta.rb100644009.87 KB603395fd67f64140a8d4c596a8c8fd821e361b1cd940f8cd4f33c0680a4b4577
test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb100644003.32 KB639fc408259b657962683068b3f09041214c930ce289e4aa1f43e5ccae0f5b44
test/unit/bio/util/restriction_enzyme/test_single_strand.rb100644005.02 KB9b3348b3e537492f8558b4d66c743dff875e19480942c37ea8f2036ca6c17d3a
test/data/clustalw/example1.aln100644003.45 KBc42d8d3ae4600eb9450f98e211f9325b84af2580cc486f333b59bfa75c28bff5
GPL1006440017.6 KB204d8eff92f95aac4df6c8122bc1505f468f3a901e5a4cc08940e0ede1938994
Gemfile1006440070 Bytes58696e0dd89d519bd2290fdb3f8fb71bc499319f2c42729c84375e5f3e854eb7
RELEASE_NOTES.rdoc100644007.09 KBe43618c69fff7cdd95536db2432e8224899c6735dbbdea6d175f5c4cd22b2858
lib/bio/appl/emboss.rb100644006.08 KBdeb9645f09998c1f6f5dbef7a97a2e5fb491328634ab4d50f09b2f1afa8ec2e1
lib/bio/appl/genscan/report.rb100644008.39 KB8e4d6cf17cfef74711f9ba6bbd06cdf35ac8b7d3e2efcc3837e7e9e55a328fb5
lib/bio/db/kegg/expression.rb100644002.98 KB8f4213871035a65826092c39a47a5f0302e57fe9a9e296f056faf76c3027023d
lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb100644003.93 KBce42561e0bb4f43c5997abc10c32684ffa37951970b54224332e6952118e49cf
sample/fastq2html.testdata.yaml10064400171 Bytes02e0df7e99dac92a855c45bc5b60db18a8c8b6ddd387208d79c9ececc9a21200
test/data/clustalw/example1-seqnos.aln100644003.57 KBb9bf2f48dee39221526a9a27260ceb4e8f04f5be561a2512d395096f7106211c
test/data/iprscan/merged.raw100644007.47 KB5eeed06ce72f5e9a2b6c1b8cd95daf17c8df82b1e926056dfc089a141a1177f1
test/data/paml/codeml/output.txt100644005.47 KBaa4dfcbc3cbbf663558c2129d338285ca1d541a29ad0104c55765b552bfdb3f5
test/unit/bio/appl/clustalw/test_report.rb100644003.92 KBce65895368907a3cc9aee545958626b2c870760947cb988bead38f85d8f9f31b
test/unit/bio/sequence/test_aa.rb100644002.53 KB15d484c50fa839ee6108254bc0e8a6551964a55a2f4ea5adcfc4d5343eebc92d
test/unit/bio/test_pathway.rb1006440014.7 KB11536830825ce1afd7cec5eaa923baa2c1717de7345f0e7d93acb7cb0ceacb68
lib/bio/db/pdb/residue.rb100644004.13 KB8dbf4c456d5ea3209fba942a5268a1961cdf36174389467d81832e0ad735a62c
KNOWN_ISSUES.rdoc100644006.23 KB42672329c2ad9331acb30f0b1f2566ba8fefc1db07ec3446695799b438808ffc
doc/RELEASE_NOTES-1.4.1.rdoc100644003.03 KBbb8a82d5abd538bd6ad8ddd0aa9b10c55ab09d09e4a9720bb86d4934d2e2a636
lib/bio/appl/bl2seq/report.rb100644004.41 KB8df8c2691cfe2544eb1ce8047169453d863d489b4bb2471ce9b99f0c291d40ce
lib/bio/appl/fasta.rb100644005.84 KB1c08a4018fc4e34f195ee25c0dfd0d25172bb9565579e68752ec51412da6699e
sample/any2fasta.rb100755001.33 KB2b781b7bdf098238d5fe0772f5cabeae4130d09755ba1c8f9fa05d9cd9338a32
sample/demo_targetp_report.rb100644003.27 KB29e1c7c9fa0b3bf213064bafb5d586133e6469196e3658aaa8e6fe0f5148cf82
test/network/bio/appl/test_pts1.rb100644002.43 KB5344321f243479c9202184d8e93edeeeb35c61153ec79332bfc8726b8a646a55
test/unit/bio/db/embl/test_embl_rel89.rb100644004.82 KB657198b3e5459a35593f8cab2f5f0eb475cb762c7f2cbaf34cc68fab3908edad
test/unit/bio/db/test_lasergene.rb100644008.38 KB67b1662f1f1003cf9dcd22755c51297002ecedecb1aecc1fdcb1c49da0014bf3
test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb100644007.7 KBefadc0c9037ad1205c09a1a8177cf60f3a59f45eea852a1892698bb69d741e6b
test/unit/bio/util/restriction_enzyme/test_analysis.rb100644008.81 KB00bb1a18e1a7a7e09c43eed2cd7cbd51d704e8de443de2f9dae8d4bde9ff8fda
sample/demo_locations.rb100644002.9 KB6d199174abe902c5fab571b53d33c856aa2e4047b823e76af4bbac253e9a07b0
sample/demo_ncbi_rest.rb100644003.48 KBede3b871491e386f854e9bddce1f08e7c05e04f36efb5bce28bfaff080d36329
doc/ChangeLog-1.5.01006440094.7 KB94b002ff7b37aee0d5e782d8177a77a02659345b7a2e8d3d0e905921a70d0df9
doc/ChangeLog-before-1.3.110064400127 KB9f6d16df3336cbca579e1fd90d0bba50878442fb5403a9ea3a7f0d13f1c51823
gemfiles/modify-Gemfile.rb10064400606 Bytes66bcd493f3b1029a3c48dfbf86772eae4438c4d176141c34e84800a066e287c5
lib/bio/appl/hmmer/report.rb1006440014.2 KB9c3e92e9f168c849c3a25c7605fd6f834884c2f60d0eaf5530a9fa5cf9a87e83
lib/bio/db/embl/embl.rb1006440013.1 KB08e0931200ec3e959cc09a502fc33803f4a228e4f5ed04761b55ef3e8134f1e7
lib/bio/db/fasta/format_qual.rb100644006.09 KB11435edd1f11ef00ae7a83405555d774386902a62d886d3261cf13ef77ed86e3
lib/bio/io/fastacmd.rb100644003.7 KBf6a6cad60a2cb34c0aa7fd9861779bcc94b35ff10ae16e12a43bf4ff51c75c5b
lib/bio/util/restriction_enzyme/range/cut_range.rb10064400579 Bytesd6eb663412027fe3eedd58b7a61893efa3eb63b717f8130c8e0d84c829cac176
lib/bio/util/sirna.rb100644008.58 KBe21606a6f658a667ddef39c688316c5f023fa9d29f19ce021f9daa93eca9ac76
sample/demo_das.rb100644002.23 KBf193aaa863e90aba9bff5f2be0ae191a552f6693b81df4b13451149ff751dc9a
sample/demo_litdb.rb10064400832 Bytes52bc6ee01104e8a5785ce9ebe94ccee7d341fa7f79b90bcde433a82cc27e4665
sample/demo_pathway.rb100644004.75 KB1ae00d528835caa4fc328830982ffdbf9aa90537a18862dc4a692dbf6c579833
sample/vs-genes.rb100755005.82 KB88f460be7dd0ea6961a364efb8ffa2037dd20636234803968dbd99db783cfaa9
test/data/KEGG/K02338.orthology1006440031.7 KBdd864ee8cbe56fdc1fbf85df596e8b7c2d6d11cbbdd8ffc17570b8cb2c9c253e
test/data/KEGG/T00070.genome100644001.16 KB2ba3a3e622afbce769db9dae9f26fd90a274ccdac4427bab461c200cae479cac
test/data/fasta/EFTU_BACSU.fasta10064400447 Bytes9a967e3c7b126c9c413e8f15136cc2ab7dc7ca4b7af3bf3a290f1213cdafbdd8
test/data/fastq/error_diff_ids.fastq10064400608 Bytesfb28be12cda772adc2ca0d29c7b1159b439472ad8383406b2be512249bda347e
test/data/fastq/error_qual_del.fastq10064400608 Bytes843acd2731c024662a481a9ff87349f4372cb407850fdd1e1b6d1c1dcc72de54
test/data/fastq/error_qual_vtab.fastq10064400608 Bytes24629e256f3ad949817c8e0c1f5e117c1d62fc64b96d74fa0b9ffb9a52b56274
test/data/fastq/illumina_full_range_as_solexa.fastq10064400426 Bytes8c7499a7f6dc5a0c6a2a8af7c5051e6c47dbc10bf106e721db50e40634925a5d
test/data/fastq/wrapping_original_sanger.fastq10064400975 Bytes6f692d81aad84c258e0dc42c6ca8dcf7b7da694c177a3e948820dd1ffb6e017a
test/data/genscan/sample.report100644002.7 KBf13ec60b9b006881654cb13344f92618f94d669cfa2fde890be41f37f3f38ad8
test/data/medline/20146148_modified.medline100644001.51 KB5a01f64a933750b644b06458086c31a1bd1b98409c74d3eab761dac1f68c0736
test/data/refseq/nm_126355.entret100644003.4 KB60a6bdd9418cc8b9bfc96a1017f412db4f6baddfb3bd9a33c17297bbfc89aee7
test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf1006440046.4 KBdb84e92dc2aacbf0d84f003593494292e8799a4677c003f6b7d19ff4abfd0061
test/data/soft/GDS100_partial.soft100755004.41 KB1bfefad740153929f2e57e33eb45487558e52da5e577f6a1c690c06f7af5ed0b
test/unit/bio/appl/blast/test_report.rb1006440039 KB1ea2ac2b06924b6922f24d73f56f321d7c933cf2167bbc296fa7b3fcd8a94491
test/unit/bio/appl/paml/codeml/test_report_single.rb100644001.29 KBcaebb93e27cdeaf36acb631d993c47baf42604ce50beca92cc86ad09d1ff7587
test/unit/bio/appl/tmhmm/test_report.rb100644003.2 KB58ff701c8d1aacc023648e8acfd3c13698b82d77097ab212158b2ef529de792d
test/unit/bio/db/genbank/test_genpept.rb100644002.02 KBaa9f5043b990172d2e47a57b577583d82823cd3da6ad0e5c21208f558c126796
test/unit/bio/db/kegg/test_compound.rb100644007.86 KB890fb8731a62a2819b41fb93a374cd9039007a1bd4397c75a0e5db028c1d4bbb
test/unit/bio/db/kegg/test_reaction.rb100644002.99 KBc7084af4afbb8495119c99989df5e0d1504ce64a908448dc8b5b15cbde1c8a56
test/unit/bio/db/sanger_chromatogram/test_abif.rb100644003.52 KBeac44e746b7ba8f459bf0e167e1c67a038a69e5be82266168ac07f4236151d13
test/unit/bio/db/test_gff.rb1006440043.7 KBe5c4ccfc810883ecee560aae9ca9fc8a1e57826b60fdd1ffbaa215fc4cb77b22
test/unit/bio/io/flatfile/test_autodetection.rb1006440010.3 KB3e2783adfecbc429338babab5c5415daabcafb19aa1fb0f3c6321b38ae1f064f
test/unit/bio/sequence/test_common.rb1006440011.3 KBd1b0d9553b83b4c833cce9f63a5e1eac728c8e86710feeb167196f92262d7776
test/unit/bio/sequence/test_quality_score.rb1006440012.2 KBc9d802fcfb641e7173a2f51717ca369376aa81b8a37170af7e09e10f453eebff
test/unit/bio/test_alignment.rb1006440034 KBeb3def9259810b55b3cd2a29a9a255717b0011a6d424c2019511ae4ad61dc6ff
test/unit/bio/test_db.rb100644001.8 KBb4fd823ac1c222b1a7b5fc65023f2de040136d0ba1a4c02ea9b8722453a7ebfb
test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb100644003.45 KBba6116356af552be39457a0aee054aaf529774d8c905da6ee399141fe6ad335a
Rakefile100644007.89 KB4a978f00cf322c89474ccac1ef6b78854558429cc23a7a96903664e344815834
doc/RELEASE_NOTES-1.4.2.rdoc100644005.16 KB6469f0d50b99f16bd67427e7aae09c7490eefefe57bdcefcda2d51c8661c5e1f
doc/bioruby.css100644003.89 KB98fdbbc2192ddabce70ca48125b00fc1bced6fadb2ea46d42e7889638a7e6799
lib/bio/appl/blast.rb1006440015.1 KB45f837cc43b54798c535f30afe92c0330ee4aa3d630710bb6987c16d9f2284a0
lib/bio/appl/blast/wublast.rb1006440014.2 KBe10886505ef1146cd2dd1abbd4cb67dcc7c58c05d04054369dc40e774ea1de02
lib/bio/appl/targetp/report.rb100644003.86 KBea6395dcc172bed3f4fefa7d6632b622c9494d6c5b4d747002f0f23a25b52f3a
lib/bio/db.rb100644008.14 KB63ef9fcaf06e37eb4e88d3040881f7689d6f99b9e75cf8f2824f8b82ff9e38d4
lib/bio/db/fasta/qual.rb100644003.37 KB50c95a33c14d14fc0f93f7fd1858ce8a547d648b297e952d1de56bc791f9adf6
lib/bio/db/kegg/drug.rb100644002.74 KBb5ef401b465659835991cb1658f078cd9d84b72a7efa7ff029d404919078b7e7
lib/bio/db/kegg/keggtab.rb100644008.86 KB8746e7d99d099528bb6c32cd2b15f075d7b51a6c6f1afc515e72a29886d7555e
lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb10064400803 Bytes4a22c7c7063b42ca96f2809acae97ace54e65ac5ea93d7160ccff2c3bef7dc73
lib/bio/io/flatfile/splitter.rb100644008.24 KB16cdfff3260ceea21e3993cb0983e4b9dfeeca0aa75cae5a4b91684b41f6baba
lib/bio/util/restriction_enzyme/cut_symbol.rb100644002.67 KB2a6790db38055526a6e31eadaa4ad293ce81974c2d98fe8e94499179d6235750
lib/bio/util/restriction_enzyme/range/cut_ranges.rb100644001.2 KB445bdf55e5fae021d47c756b9c9eca99788a9b93acb20a2c01d2ad1017acf188
lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb10064400935 Bytesc987a84db406b24885ec99a03481d065750f77e6cc2eccb715f8300d6863b045
lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb100644002.48 KBa1de1d7275e4f383e76e4077ed0df18f4c9caa801bfb5d2fa30754fc3a36e3d6
sample/demo_aaindex.rb100644001.33 KB9a4732eefb18e0b31d258319c33a103f8e2e0a976e812a1f8f834efd417e155b
sample/demo_hmmer_report.rb100644003.72 KBe59b19e3d17c68adaae6d0e7d432531310cad2b1bc074e8d593bed378f3bb5a8
sample/demo_prosite.rb100644002.12 KBb5d1ad86818fcd67e730037829d480ac976f1c4cfdb64420d67cd481809e0ac2
sample/demo_psort.rb100644003.37 KBd399f80d7e1919ca8189c90a6ee7b4299ac90a4a92c19f21b3357b214af0baaf
sample/fastagrep.rb100755001.78 KBcb2f5248e1106048f2428cef80577fbab52ec65ee81ae33dbfb5de02ee90ecbb
test/data/fastq/longreads_as_sanger.fastq100644008.19 KB9b1f6ac49d2a2bfc60170ac1edf5a772a3bfa1dd9d731d4f36524f6c7f9321f6
test/data/fastq/sanger_full_range_as_illumina.fastq10064400550 Bytesdfd416a2f4bfe648e968c915f322e98123eaf13cc7c3bd4344323471cf01ddde
test/data/fastq/solexa_full_range_as_sanger.fastq10064400450 Bytes10b0c1a68a40b726229f23f0989637e6479513965bb9c450ac81eee1ce796808
test/data/fastq/solexa_full_range_as_solexa.fastq10064400450 Bytese6c95762306bf1cbfd7bb952215fc20751caf2448c083f6fdf4414dc8f96e8c1
test/data/soft/GSE3457_family_partial.soft1007550045.5 KBdbb03aadc6b6db0a5a80b05b6b09ace4725fbdbd2862c6925d0a7c72b68aaef3
test/network/bio/test_command.rb100644003.12 KBc1f17a34cc5a8c4cffa856d3d0b73871de4a174d42e2389400e6a25cb907c422
test/unit/bio/appl/targetp/test_report.rb100644003.72 KB9d97b77415866f5cf4bff800c16ac6b4aef5ee0cc331366af18511b383198476
test/unit/bio/appl/test_blast.rb100644007.11 KB5656869208d151f92f53a1f3b864e0fece23de7a41f874a5be67674cfa216197
test/unit/bio/data/test_na.rb100644001.84 KB29a121ecbaab5dce5952e9a9a6a50041c9ad85d1b1fcc5b6eb84b986fff71e46
test/unit/bio/db/embl/test_uniprot.rb10064400754 Bytes4a1a85b00ef7bbaee0a2f7da34e76d714983db5ca43810d23882dc8c614cf253
test/unit/bio/db/test_qual.rb100644001.68 KBb194dfa258bce7f04cd7f3b755d6bf133c97a27e6d41eda18bf3bf50ce9cfe29
test/unit/bio/sequence/test_compat.rb100644001.68 KB755f9dc47663fa487cca44bf74af2398d35f371e52f3688b4deb2b708cc6cf6f
test/unit/bio/sequence/test_dblink.rb100644001.64 KB7198559267239df7b1ff7f48c35da00f3044acd7201e92128babcf19c2472d01
test/unit/bio/test_feature.rb100644003.16 KB113c5a97d4acd60782dd8f9f29522c34673ae4001600ef1a2b6aadc41d1fc675
test/unit/bio/test_location.rb1006440022.2 KB280c4dd0fe07544fb6e6dccac33405d96d6c9b294be914bf345f6835a11a08da
BSDL100644001.25 KBa5e3042dacb53eebda91f3b1caefbfec8307711df8c4ed1ed20e4e97c43307a4
lib/bio/appl/paml/common.rb1006440011.1 KB874eb1b7ea612e4370d66f8db93a908c95041ca61d78cf639cfa393fb1d6501e
lib/bio/sequence/generic.rb10064400396 Bytes0ae26b5956283a7a6f1516712532e836bf400a2880a34f0b89fccc890de4e323
lib/bio/util/color_scheme.rb100644004.94 KBa2e614c3205ad4e364eb422b703efe3184afe8261515565588406c4a17ecbc30
lib/bio/util/color_scheme/buried.rb100644001.24 KB9904524d8f999ef83de1568d72809c1999cece53397c655ef8776a78a38eafa9
sample/color_scheme_na.rb100644001.94 KBc67863c3aa8fe4fe9132dbb58589a4f5cd490682c28c8509d245b89aa9d926a8
test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb100644005.07 KBf8fb8b389728d100a83117ef13cc8f1786a809ee9a0b96454f0cc86f333496de
test/unit/bio/util/test_restriction_enzyme.rb100644001.15 KB85ee7040f13c29220072ed4ea1142685cd2ae90ad3cc2c7e460fe2532533bbbd
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb100644001.47 KBbf40d893499726b091be88692cbb7a7072503cba1528527f34d0c2fc5fd7cbc8
README_DEV.rdoc1006440012.1 KB1296d49ce52524b511e85c7c07284d13f8be58ac579bc034eaaa974aea30d781
bioruby.gemspec.erb100644003.09 KB60b07e2697687b8d6c80141c612890304e7931a3e6757f394c382bccb11c969e
doc/ChangeLog-1.4.31006440053.5 KB80b8c972b72f3dbd19d4f050137b42f60e3d438796abfc9bfab173fa4b11b43f
doc/Changes-0.7.rd1006440012.8 KBdc32dba9fc065d700458cedbb493c30ca341afcd4541e53ad81b956cb8ee2263
lib/bio/db/sanger_chromatogram/abif.rb100644005.16 KB35137a2bf5e99400ce8f9f7ed58cb70ebb2263dda5db2f91d7df9c1bdfa24c09
lib/bio/db/sanger_chromatogram/scf.rb100644007.39 KBf8fb3148e3110577eecd8852635f0a9d4da9b8117f0cc7c9a833ef1d3eb9b4f5
sample/ssearch2tab.rb100755002.24 KBf48f03ed7e929175411bdb75df185c16b906a9fd5fc0f3e7c8feb1a95536a25a
test/data/fastq/error_trunc_at_plus.fastq10064400548 Bytes785fe4189c44bb5503b51a9e26ac58127cfb8cdea2ebe244213d2bf5deae7b0d
test/runner.rb100644001.08 KB81346e8c3d361ff763165a93d34633fab72d87d4002180f2847a1b1678b8080f
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb100644003.12 KBe0e643a36525596fa30b8c4d5831ebdd4d5a3dc3ccf1df72281abfeaeea06a56
sample/gb2tab.rb100755005.65 KBbc7816d5b592ec40701d58978e0c94ffbdf63156a502c685be78ed54abdb0d0e
test/unit/bio/io/test_flatfile.rb1006440012.9 KBcf5883c0606271c205719b03f62cbf7d69f2df717622ad2b7c8a7a9177b57d39
doc/RELEASE_NOTES-1.4.0.rdoc100644006.14 KBd445473dc2befe85dbf029d4936c907b0ddf4f1ac56dd9e436e11e1250da25e2
lib/bio/alignment.rb1006440073.3 KBda8f7d2014c10029443383287799a38d3212bc4e8b5733feb9fb35db8f0f3e33
lib/bio/appl/sim4/report.rb1006440017.3 KB9482280372a299c66ed8a073cbf433db28caf5a9fa7d5257f7e2312aadd38ce6
lib/bio/db/kegg/enzyme.rb100644002.88 KB4ddd7fb884c937f033ccfa53c3534c99587589cec3b1189fe61ce65a6c93e6e2
lib/bio/io/registry.rb100644007.38 KB9548f9c05e41bc653b1c149f484a174dae94346cc02fa1564deb9215a576f9a0
sample/demo_kegg_reaction.rb100644001.47 KB3b5f4b0c869458395fe10b94ad20139efe265c5d4312cf4f7e7f7dfcb7904987
test/data/fastq/error_double_qual.fastq10064400669 Bytesbcd0f39312b6629a9bcbf5e260bd99f2edddd27ecb77df91bdeeda1bb7d351c0
test/network/bio/appl/blast/test_remote.rb100644002.19 KBa84f887b55dbff69eaa7061de5fde93288408d6f78260184796855ec6c18724b
test/unit/bio/db/kegg/test_genes.rb1006440010.4 KBa63ede89d796d398e8a28038599bb1732c405f9db55d22817b978dca88c6af17
test/unit/bio/db/test_go.rb100644006.61 KB8912b4976008031c10cea41aae5e9542a758bcab32876274e541d70a296e8859
lib/bio/appl/blat/report.rb1006440017.7 KB1c97d4b9deb9901ec00ac643fd795812aa9bf3c687fa3f89bab91b7730bb3376
sample/gbtab2mysql.rb100755003.99 KB92b5b3f0f9ab26f44e193bd51adca9ad1c41dbbeff05cf7395cfc02d40fd8624
test/data/litdb/1717226.litdb10064400560 Bytesdcacd8b0a50aa28d404086920e9f9caab8beb064499540015ffb2d9ee6209c98
test/unit/bio/db/test_aaindex.rb100644006.04 KB116a77856adc3b9543438484abf02af49dac9f184b18b0b6418b4277517a73f1
lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb100644001.25 KB808a257e3cb7a0d06eec96f464c3d79ae78a0eb1d8537b5c62c9bc39ec0fe7c2
test/data/fastq/error_qual_escape.fastq10064400608 Bytes12659079d3d9f9348990d3c540988d3dd21dd80a5abebbe9527b5a24eb2a3e2c
test/data/fastq/error_spaces.fastq10064400628 Bytes478e3f6c09d4f4ac82b68b3607c7d5860fb0c3192b7f04772694067301e6e767
test/unit/bio/db/kegg/test_module.rb100644008.84 KBbdd11e1a61c1d33f82e37c1635a2cb5c6030eee76ed0a89f4b67180ebbb1b739
test/unit/bio/util/restriction_enzyme/test_string_formatting.rb100644001.75 KBe200dbd83a5a573706039647aec09795c47ae71089a0796808c8fb232e015238
lib/bio/sequence/quality_score.rb100644005.84 KBc2d70f1176a0963fa87abac2a9e66d5e06e36bb81a2bd273f17eb95b0901efe7
sample/demo_psort_report.rb100644001.42 KB2ed41494c85b0f89a81c42c485740ec1220c0e2a82618a2c42365a5dd6c59141
test/data/KEGG/C00025.compound100644005.2 KB837ef41867587872d0b0a53f66f7b50093249569516e0f815721b722b0f32871
test/data/KEGG/M00118.module100644002.16 KBfe02348b75b75f0ec88b67e2c0c15a8d193807cdfc7706c978460f1ecfed678b
test/data/KEGG/ko00312.pathway10064400710 Bytese302cc5b64a92abca4750c513474dc8fc3927df12b44f2e6d18417c59926742b
test/data/paml/codeml/models/aa.aln100644001.35 KB1002a03b17cedbcd23b826f98da8e2f957868ee34bbe635e2a3bfda32d57a063
test/network/bio/io/test_pubmed.rb100644005.08 KB3743998a5bd67825198a062917e686d2e0ddb404eb283da816b89f33fe25fd41
lib/bio/db/transfac.rb100644005.88 KB3ab86eebe4675524c4394743cc01a9658bb4249b233c1a3d481ad74f45d2d6e9
test/unit/bio/appl/meme/test_mast.rb100644002.75 KB853e762224db2d84f48178ab9dd23ff9f3b43079f0c927c2a7e353e3ce8407cb
test/unit/bio/appl/meme/test_motif.rb100644001021 Bytesbb29d17b6cbf8a5918072b542763d87cd8223f86d7c6f14f27b220c97b5fb4ee
lib/bio/io/das.rb1006440011.7 KB465d0856d73bb254e5e94124e5d52d01fdee55200cc9af2cb1bf2f6ae6158168
test/data/KEGG/T00005.genome100644004.8 KB479358faf150aa9279296b0829b0ff4e9ae6a206e75bc3620f6838278ce5b6e4
test/data/genbank/CAA35997.gp100644002.01 KBb4b7f655fe65d35ea050d4d0d8fba18caa5bd156db50438f6be0b3c480ad95a2
doc/Tutorial.rd.ja.html10064400113 KB86de06d8efba3a29ab7f5b38ca50e415e91f9df3dd4afa2a12090cce0c18da06
lib/bio/io/pubmed.rb100644006.28 KB32e55d50fb999afa66a146de25e427300aa3d06c73cfcc42d06381b58a2bd9ac
lib/bio/db/fasta/defline.rb1006440016.4 KBfcdfd55ef2a8d8cd372434d71e0eb3b0ccbf401c9975a167925082ee9ea7068e
test/data/meme/meme.out10064400190 Bytes42d3f2d71843fb9cbc0a9d3b3db6e2e17655f06bfa0a2694c814eeafeb49fde0
test/data/paml/codeml/models/aa.dnd10064400173 Bytes568feae9329e4465befc5f47bf9f76e71e3d35b6e787ac26195c9ae97c7af215
test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb100644002.39 KB3fab574dbc9bda283038255d49f111c16d0ac08ba3abc9bc71bfd6f7775ef3aa
lib/bio/appl/paml/common_report.rb10064400844 Bytesa6bf1e607f9d94f754900c1e5d14d1a42dbaf70b9f123ef8f37cefd5bcef7163
lib/bio/appl/sim4.rb100644003.3 KB0738d0d14c2f1ec99a5125831ae2ee3c3de5f09ce6489ee50e9eb82e7d5f2662
lib/bio/db/fasta/fasta_to_biosequence.rb100644001.51 KBbe1fbf4bc481f11772ca1961afb6187ee7a40073254fefad0010a42d88a6d731
lib/bio/sequence/format.rb1006440010.4 KB53b39789a0a9a69f55ec1c2e22db861b38a827f6625ce17f2cda5e9ab1a14412
sample/genome2tab.rb100755001.65 KB5325f258867cc7f73710c9773bde73c12dbce2e4edbb3e2e8bc91c887cf06ad3
sample/gt2fasta.rb100755001.19 KBa2276c062324475448793430ead285622080fba27cd386fbdef8008218a5a727
test/data/fastq/misc_rna_as_illumina.fastq10064400774 Bytes8c421caeb94ff3a46da42307e67f8ad21ef02763793f2a695872651e2b203635
test/unit/bio/db/kegg/test_glycan.rb100644007.91 KB726299eccc10984283821a6cf97491ff56be7d384e536a26b26d4d78d0ea8c06
test/data/fastq/misc_dna_as_illumina.fastq10064400767 Bytes8c059e0f208320e2443ff5ae1f5c6c2be741a38f48caaf967c269ae264b35a28
test/data/sim4/complement-A4.sim4100644001.28 KB49975dc65d349b605448e7248be76ae2f91fcab52bc9ae14e45d202bfa21f244
lib/bio/db/genbank/format_genbank.rb100644005.27 KB05eef2f3b2a247b9715a8b68f921386486b1e3929e290e6a62b9d435e81af02d
lib/bio/db/sanger_chromatogram/chromatogram.rb100644005.48 KBced38af257a97fc6ca02ad8f4fb94354bf662b286da6d1e743b0b9842e1deccf
sample/enzymes.rb100755002 KB6e6056acba8725e95dd245dc889c3f5d388001b0111923bc973edb6600fecb53
lib/bio/sequence.rb1006440015.9 KB7508f4467236cac107728cfda58dc1d015a741539426251b6943fd711afa43b9
lib/bio/util/restriction_enzyme/sorted_num_array.rb100644004.39 KBb88d7eb04fa5a22c1ba80684bf2d2eb0631fe23642e05195169506b061099d97
sample/gb2fasta.rb10075500924 Bytesc41ea6c950dcc6d8295e292f7213b8460d71f9f7819e6e02a688ef350e270dcf
test/unit/bio/appl/iprscan/test_report.rb100644009.07 KB95723d81f560ab7570ebfa9557138a5b4968d82de19b5c6cb19447782243bb8a
test/data/fastq/wrapping_as_sanger.fastq10064400963 Bytesf8272a035e8908a7939f525de403563f726b577e37bae419aae8de55bc4502c0
test/data/fastq/wrapping_as_illumina.fastq10064400963 Bytescceaae4b9273ceabe155ab40724f96d56c725b920fa94ddeb0a0c21f9fc8e0ae
sample/demo_pubmed.rb100644002.99 KBc3160b959f0d89fbc64be4974461341d2ccd14eacd9d4d9c9c97bf62498522b9
doc/Changes-1.3.rdoc100644009.46 KB804d1a8e27eba9db6f0a53589bcd3613245c841d1248319afe36412b66f394b9
gemfiles/Gemfile.travis-rbx10064400128 Bytes82195fd62cffc4842433198bc0ebfa5f3cea9840a902653da7d6438312c18071
test/data/fastq/longreads_original_sanger.fastq100644009.24 KB09b5f250b24d2744fdcfb49d5372ed92666e4d6d3e694a466509e2f179880261
lib/bio/appl/mafft/report.rb100644006.51 KB1d4b4cfee1e66e52d7c39cb7f3086148d38b815d44f843f33a30d4042e42db33
lib/bio/appl/meme/mast.rb100644004.21 KBbcc8530e6703d5ede51c124e9818896cec6236dca82dc44ca4235f98763ac1bf
lib/bio/db/genbank/ddbj.rb10064400524 Bytese6feabd45f3ffbb79d7158a4e3b784b504680e282a63cf29429f6c41fe29f6b4
test/unit/bio/db/test_prosite.rb1006440018 KBb244e49a2fcd841894ec25a9ed3cacda768f61575863a44f2edde1f3ff94e921
lib/bio/db/embl/format_embl.rb100644005.67 KBacfe0de3fae62f716606ebe369128dd9a3d43723907c55692218d41b74579353
lib/bio/sequence/common.rb1006440011.4 KBb532d8770361c39636211df61335bd46abb5baf69a030776e0fde7718c3beaca
lib/bio/db/pdb.rb10064400517 Bytes095afb155fe328583cd1f4f2d96f7c656fec94a2ece3b5f3b1e1df86b6ec7c20
sample/genes2nuc.rb10075500955 Bytes0caf11a1a36cc66aa4dfcf92ff53af12ce4990b663a2096d907243b736b67267
test/unit/bio/db/test_litdb.rb100644002.57 KB1a0d26d636873cdb2be54c4b3388cb18fc49919b7332d449ff78f1c4afc7e00f
test/network/bio/db/kegg/test_genes_hsa7422.rb100644003.35 KBbbb1d40e26d46836f2288b1e062f806a2dec26159294d740c0855eae7df4fe4e
doc/ChangeLog-before-1.4.210064400193 KBc22b7909f473df1dd78524ad9f438d1be7b38de3c84b80af409772b319b2cf50
lib/bio/db/embl/embl_to_biosequence.rb100644001.7 KB68591ecd39e1f856e9c55abd8b471514f64db35b8e14ef39eb3a1470c1e91096
lib/bio/command.rb1006440029.3 KBa7dcd0c53372140c5ea6666eb72c62d25c407e3b06e0ca80ded71ccef958345f
README.rdoc100644008.52 KB76fb656db65e42b92d9b1869e32792cb1e1d3bf6e18b4fe922cca06b85e40b56
doc/RELEASE_NOTES-1.4.3.rdoc100644008.55 KB59170312625e843ad462eca84e7d7e1a0e37951c628ea4f11d4c85ddcc6db083
doc/Tutorial.rd1006440047.4 KB10ef70d395eaef8088b459fca34aa8f663780f86a9cd0d93e07098329589fd1a
doc/Tutorial.rd.ja10064400100 KB5123f4c8b32ae4abf3400a7e0c9a36d4a15f69c8b8ad69fbcd68bf60e4f8f991
gemfiles/Gemfile.travis-ruby1.810064400111 Bytes0f7a91764dc9e0183471b039378b1d73c6895044d0a1039e6654066c42c2fad2
gemfiles/Gemfile.windows1006440070 Bytes58696e0dd89d519bd2290fdb3f8fb71bc499319f2c42729c84375e5f3e854eb7
lib/bio/appl/blast/format8.rb100644001.94 KBe5de459c710c3a819f17ed3f6e37ff708dd34b040ab063191418911d01581e0b
lib/bio/appl/blast/report.rb1006440018 KB86d9fc9175ffc7ec4ec04af26140be437186eb2f533abea96872c65af120546a
lib/bio/appl/gcg/seq.rb100644005.41 KB4aae0d8bde943bf48bd28128c9a9206ba0d75a437420f3023c58d0035edc7f40
lib/bio/appl/paml/codeml/report.rb1006440017.5 KBe68c2fb738adbb7e5acfc86c413e64407e0ae99f761de934e195210ef0e2a94b
lib/bio/appl/pts1.rb100644006.07 KB4d4915e5355ac18703ee51cc9fd55d9cd9721019acb425bf45da1d930c70c43a
lib/bio/appl/sosui/report.rb100644002.23 KB9bca0dd0132c97b442cb577b0823dd0bc430d45dfb7d3a746ee1e30c877bf72d
lib/bio/appl/tcoffee.rb100644001.46 KB5d6065494772947211a2b8d1b5d50e84aae79c591238ba640f86fdce51a2b706
bioruby.gemspec1006440023.1 KBeb656c23cb25ad7a5defb5cfc05e23da164bab57cba2096495933cc9c5295207
doc/Tutorial.rd.html1006440051.5 KBa53112b94e27f70b7dbb440487cd0bb36c92fa71651fd532c515fd87d7d3c6a8
etc/bioinformatics/seqdatabase.ini10064400492 Bytes5a3349212609a0a08896f7e9bac2360bde385d8e94d177b73be3a41a32306e04
lib/bio/appl/blast/rexml.rb100644004.14 KBbfd93b105ccd8608df03e69076b80165ef72b4c7578922a779c3071ad364bf0f
lib/bio/appl/mafft.rb100644007.14 KB03c8da2d5aef2ff37488e33f03a31697a9e91590840ce2221cd3cf83bc5e65dc
lib/bio/appl/meme/mast/report.rb100644002.46 KB76c792a5489122379fb2babc428df70a6dffcfb0c98c36ab84b4377a601d6ac7
lib/bio/appl/paml/codeml/rates.rb100644001.9 KB12567fe7006ba7132a429618989bf69bfe47e2ffbdc9b5d86c06b0bcb91bda5d
lib/bio/appl/paml/yn00/report.rb10064400644 Bytesbd7d8221c4272671781bf8f07a4405f30bb0b1ac804c0077da34cdb361678fff
lib/bio/appl/phylip/distance_matrix.rb100644002.63 KB24455644af9afe549c082972df362c5caa3d3eea3db29b2298f975a05d3c6626
lib/bio/appl/probcons.rb100644001.16 KBf8899e8ac6e99ecf62a793507c2e51c4be2fb3a69f0c44e02bec869a9e3fb867
lib/bio/appl/psort.rb1006440012.1 KB57e9e08d484f82b9b0481fb4a045b6279b3145655d6f58b71695e191d9e913cf
lib/bio/appl/psort/report.rb1006440012.4 KBa6d4f66696a5cc9a34df56e9c6921098ae27f2c0e38284e58ceb1b558cdac8d9
lib/bio/appl/tmhmm/report.rb100644004.3 KB35643d70c379494d510a253dc0cd1807e9cf9690b77730b639bb34bf25523806
lib/bio/compat/references.rb100644003.59 KB2c9b0a6ae3aac34d26693af51bdfaf847df0d4813d6d8984f9c11de8151fe744
lib/bio/data/aa.rb100644004.59 KBbf576ddcba497d15cd6c5f8afe632c6b9cf38de7251f9071c252b0ba93f2054b
lib/bio/data/na.rb100644003.62 KB850ef4c7403ac98b365d1988c407c61b9a3dd4b5b6762baec2b037bb5066553e
lib/bio/db/aaindex.rb100644008.84 KB465cdb104eb7cbf0ac2dc1335c42c7d6567dd7fac39146c0f51d7cdd2529cad6
lib/bio/db/embl/common.rb100644009.54 KBcc8f8e4753c95b0f6a57aad786eaeaad97561bff85c5525454128413d40b5258
lib/bio/db/embl/swissprot.rb10064400542 Bytes6342f1da2cc42dc0f4a86b5f3d5cbf732df92cd99423016b590dcb4345142ddf
lib/bio/db/embl/trembl.rb10064400523 Bytes22624086c24b46fed4ff3b4783465c0bfd3918a6e90cf1bba14c0b3dfcb3a300
lib/bio/db/embl/uniprotkb.rb1006440040.6 KB92b60bb0dc775876073eddeec50324bb8c583baa9bffbdc5596c33b1a7afcdd9
lib/bio/db/fasta.rb100644009.16 KB3274262b991fb8e18cf467f750aa077dbe0458262af5f5094d03b0fa82bfb804
lib/bio/db/fastq/fastq_to_biosequence.rb10064400900 Bytesd54dd813f68f84101914ab4790e19d16df526a577d33f2f34e273d8c5ddf9696
lib/bio/db/fastq/format_fastq.rb100644005.34 KBf166e399a02954c34ae024c23d6147c40c553937d41c933c045e42a9f21eac4c
lib/bio/db/genbank/common.rb100644007.49 KB7675a42bf17ca546b5b7bddcba14002a5af7d1aa6f7878beffb681cb5031cc9c
lib/bio/db/genbank/genbank_to_biosequence.rb100644001.75 KBf09815c7600e410e67356fddcf4ccc7f7c1894b1903a942a5c86cebaf1d36413
lib/bio/db/kegg/brite.rb10064400639 Bytes88a3057e5f31e1faead4b282b0a6ff1a1806f388cde96869602eccd834ce6e9b
lib/bio/db/kegg/common.rb100644007.04 KB1d82681f5af2225323853e320096ad29dccd445c0f94a58be5642b5fe30aec61
lib/bio/db/kegg/genome.rb100644004.84 KB5ca081daa7eb5d032d79a9f19cd8a262e4098d07f196aa89ed5ec3ba7d458a80
lib/bio/db/kegg/glycan.rb100644003.02 KBde0c9aabcc82cc881f0c3bec1245207f1e5786866fc0b80f463d16ec9332c528
lib/bio/db/kegg/orthology.rb100644003.22 KBf59f9e6ba2c2bbedd763454a628047a6064e5f3624be070785a55de42510c861
lib/bio/db/kegg/pathway.rb100644006.05 KBac160959b42b4c087455ab26926230fddd8b4645fb70978974aff41cf641a926
lib/bio/db/litdb.rb100644001.44 KB87e1716604ee85e915b579384dfc1cb8b9038bd94f4528e80e4bd18c1835fbb8
lib/bio/db/pdb/atom.rb100644001.68 KB61ccec828daa470a6ebc7fb698c888b705cc9bdcf02001205ce5483e04f5517a
lib/bio/db/pdb/chain.rb100644005.55 KB75da2521747828be44c73145c710a6d1535466dd0e17fa1c81561edcdda49993
lib/bio/db/pdb/model.rb100644003.56 KB8f6c635d43d53ecb8704538886d334dd633ac74cc536776593868477d22b1818
lib/bio/db/pdb/utils.rb1006440010.1 KB745441ec3af231ef5ceaa1c4b2a9d1cde4b809460c6bd7bec724c29c870bf9d3
lib/bio/db/rebase.rb1006440013.8 KBd5913b0ba399fcf4f694e7efab6be6aa09ef5b2c449be4ec2b1c165bcfae7ebe
lib/bio/feature.rb100644003.92 KBc81e5b88bd493dd28a434d6b7c90381bf1bbe1eadaeba28d826bc1d615e6dd91
lib/bio/io/fetch.rb100644008.47 KBbe8245585427d98611cf8d1ea1f37e5e1f6afd48b67dd424a495fcf42d8eb73c
lib/bio/io/flatfile.rb1006440013.3 KB84792c667f395994d596ffed28458790133c913524acbe3f9e65d70cbd023d5b
lib/bio/io/flatfile/autodetection.rb1006440016.5 KB66225091db1d345efa5bd726f73be3759c8c25c0e50700bb202c0d234f8cfe2e
lib/bio/io/flatfile/index.rb1006440033.5 KBd73e284969629cadd7d745abae567d92ffe60df0e76c2dccf1aa498314546b23
lib/bio/io/flatfile/indexer.rb1006440026.8 KB07b629888b34645ac50a2b011dcb61506c655648b79580040cead344291bce5b
lib/bio/io/ncbirest.rb1006440028.9 KBb11b32639908c0ce9c36abf990ec306024d326d42b27d2ebb29a3337aa9bcd15
lib/bio/location.rb1006440026.4 KBe7abf505e0ea1707da5318d0cadf9fb91c1068ecc3f9fe89c26992a8cd606ef0
lib/bio/map.rb1006440012.8 KB6cebe3741e51ddecc3698a644e8b3d26ce79c16bf6c86b6342b01b3d6be5decc
lib/bio/pathway.rb1006440022.1 KB8beb60a627e783c82aee91c7566f4b4f5255ab4df6c9f287ccbc878f2c97b94a
lib/bio/reference.rb1006440018.7 KB6ab8b77b9542615a3117e4abec8a53f7ecc6a6cdb02664a39716d2af5c966664
lib/bio/sequence/compat.rb100644003.59 KBf07052c60c6012554e3c687791f0cd87d77962100467b460cbea62e2594d3c41
lib/bio/sequence/format_raw.rb10064400434 Bytesa6680735e8c2ddd6ffb563e2197230baf44b58e6f8e1964dcab3fd0fd00b937d
lib/bio/sequence/na.rb1006440015.7 KBeaa33e3a6df37bd971cd0eeceb12749d346337f486d13d03e5bedae9b4d6936c
lib/bio/sequence/sequence_masker.rb100644003 KBabc2025635a695ff52d0f746c035e16a2369da9c08c064ea5dbeab9df9e37d22
lib/bio/tree.rb1006440025.9 KBdc30e3e3b4581e18232c462db9f7cc9efa8332cb2270a5439b3eef61d2138bfd
lib/bio/tree/output.rb100644007.7 KB17ea33c97e003b34b9c275dfe4fa76db47d85b93d7dd551a4e844fa57d6db1fe
lib/bio/util/color_scheme/hydropathy.rb100644001.34 KB8b827c40b823eb57874ecf65156a8ad9ef2ed1278be7050e3e8e7ba5f93061e3
lib/bio/util/color_scheme/nucleotide.rb10064400690 Bytes826ecc72308f879c325103e36a5dbe51fe67ec5b9fcf32e73c133ceeaf80376e
lib/bio/util/color_scheme/taylor.rb100644001.07 KB1af407d819e588fd266b4076e08849c3f7fe6211cd9799b8db2126286ee5e17e
lib/bio/util/color_scheme/zappo.rb100644001.07 KB4fbe84b2835206f44f0cf7ad95889c7c28f4a207ed015f86436dd5e47f534ce5
lib/bio/util/contingency_table.rb1006440011.5 KB25c43e63255bf3fb6dfba582a62843a199865a3a92e954c526c3d17d9cffb6ee
lib/bio/util/restriction_enzyme/analysis.rb100644009.64 KB48976b6810297a7cef36018626d762f9313ea22da0dae58ef69dc7a6b1297f67
lib/bio/util/restriction_enzyme/analysis_basic.rb100644008.21 KBb8be9dc6bb6b4ffda522cd6970e1ff894773472c20a7f2e987d584b53a4edffc
lib/bio/util/restriction_enzyme/dense_int_array.rb100644004.26 KB59b4af71044e7e56f36f9e25278e98b3f080668ce6c69be2921e0266e1bb37f9
lib/bio/util/restriction_enzyme/double_stranded.rb1006440010.6 KB7bbb2d56b33b7113fe61cd4912471b28f34c4c3f56d039043c8eeee91322aa42
lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb100644004.2 KB4c9f832512c7bd714f3519f2e4cbcae641eabe20b861d2a2b5b05128306b6e0d
lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb100644001.76 KBd0b69341d3850ad289b3989854a790f04002e1203b8db371d72a7891accf2686
lib/bio/util/restriction_enzyme/range/sequence_range.rb100644009.4 KB60b0dceb2416e6e37d8f7687d201048a85e0d714319005d9fe688f840b82f617
lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb100644009.03 KB40717e8a47517c716bdde2bd5cc5bf3ee16e04c82a708b48a1d2fc2e03408cf1
lib/bio/version.rb10064400854 Bytesd6fe4253a3f9ac16b7e8aaff545ee3bb9e3e90f50f36c2951bbe33893a3a403a
sample/benchmark_clustalw_report.rb100644001.12 KBa23f1d4813e8b2bc1c36f92e8a78aacecbc076d674c4f31fa94f03441f8ab0f0
sample/color_scheme_aa.rb100644001.75 KBa634ced7a30fd3804a69403f6e6dcbcf1faf23604a2bb154fb99ea14d7c3f33d
sample/demo_aminoacid.rb100644002.92 KB5d66a56b5c310f5bddd0e2440baa20cf5a2ca1013c25d5b90b05c3f85130b7f1
sample/demo_bl2seq_report.rb100644007.57 KB0ea9c4221095bb333fc585aa330d12ab60677c96b849aecaf72f2a4edda8e921
sample/demo_fasta_remote.rb100644001.14 KBd3333a88bd43f07419197e1e93621cf95cf7a8683738da3da4c54740250a817d
sample/demo_genscan_report.rb100644006.05 KB3c4587e3a6e4bc54c8508e35daa374152e1871687fdf1d80823c78a81fc8cb6d
sample/demo_gff1.rb100644001.18 KB971afdd41ea7679d9cbfe7ffc1491a4d8d75e71cb0926471eee54e11e3f1bb85
sample/demo_go.rb100644001.96 KBdcea1de08e22bc7963396a1dd74e7cec68feabc3a4a995968921d70cbab33a93
sample/demo_kegg_compound.rb100644001.24 KBe9dc8cc8a04054bcc59f1b07f479771dc26ec51fd0aa8f264299655d04957f20
sample/demo_kegg_genome.rb100644001.44 KBf929c3029ba2de4487f047221a1059c43c972467687be02683e250ceac6d2255
sample/demo_sirna.rb100644001.37 KB4aac4578346e1a643757c55e1a30f0a3e1b891725d5225a5365ea82665e290d3
sample/demo_sosui_report.rb100644001.87 KB450026b68483c8a78bce3df8be796b49e371c137e4078c9a39322dd7698dd600
sample/fastasort.rb100755001.75 KB1b62217e8944bd9815b230caadb3665dd82d70885ef67643795c21e616a8a831
sample/fastq2html.cwl10064400384 Bytes856e6a7025a5933ee0f54392ef16f6b065e170bf1a0033becf82ee523e73b256
sample/fsplit.rb100755001.11 KB400c70b8905f27f74fd581c8c9accf5ab24748c9725131890d3e8a560dd4b80b
sample/genes2tab.rb100755001.73 KB4d160b473fd20374635ca2a04130913b0c02ed3b94169785727f88c13d14b5aa
sample/na2aa.cwl10064400382 Bytes03da2ea81cff4b35476781e354f966664324c6e00e8db028a8d63680ac014b9b
sample/na2aa.testdata.yaml10064400196 Bytesbeaade97bf2cb96bc5ca343e80f14a989575374d3e1b95bb34314f0d2db30aae
sample/pmfetch.rb100755001.35 KBd5384d2b53695c0f2d2b15071fcf6d618c6d1c95baf1be7f16af09e14295b500
sample/rev_comp.cwl10064400385 Bytes07a28321e991d50a90ff919e18bf6d72b5e3c6e2cc61386567882728f4867730
sample/rev_comp.rb10064400459 Bytesfe9e132df3b4083b0d3b527977e9933aae4685eedad3fe3e7c2edf83b205f635
sample/tdiary.rb100644004.63 KB7e6c6074a6486cdb0d1022f17f4dccc32d3ff0491457e0bd2a9e5e015b788272
sample/tfastx2tab.rb100755002.39 KB166ff75261d96454f297b3986dd16a154baeb5be15684be68871ba147e73ee87
test/bioruby_test_helper.rb100644002.32 KBd73db275a0f04547b7caa393d326d61f3fa72835fef530540495115ad87c46d5
test/data/HMMER/hmmsearch.out100644003.67 KB575ce8e79d16903c9cf7670748e88bad399066ef5b9bb35f93cb36298d76b8f9
test/data/KEGG/R00006.reaction10064400730 Bytes74cfc3e7fb48400b5dcbbafd58647809acb42fba4aaf5fb53dc83c901269b9bf
test/data/KEGG/map00030.pathway100644002.8 KB0caa06a4c62491f9ed9e9d0b87a6ec31f1ccd8cc0e9516975d5affea68d450e8
test/data/TMHMM/sample.report10064400909 Bytes9f86ea10faa13634881100b73613287672f62c509903768c33ac1d4d4cda4b4c
test/data/aaindex/DAYM780301100644002.04 KB20b2940e4d45f6b2710ca0295998804233dd8407f607a8803dd428fdf82a55da
test/data/aaindex/PRAM900102100644001.08 KB62991a1bd9b197111da30dd3bd8f2a637c435778aef8d2bbb548c5e0fa8ea69d
test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq10064400984 Bytes7f6e883493ac3be2114dfe4794e4a324bb67e7e9064c211bed60a6527c783b33
test/data/blast/b0002.faa100644001.02 KBbfd37a1019479f9388ea3c0151097176337d608993f0d0d1b6e0c69ef7850c3b
test/data/blast/b0002.faa.m81006440056 Bytes6c329cdca78f16508223e98bcbe25cb26e96d8e24180439e1ca913034fd261e6
test/data/embl/AB090716.embl.rel89100644002.49 KBac5f6d55a30fc5f050f0d8ab1f50fb206707385e7b8434daf02dd7ed623f55a0
test/data/fasta/example2.txt100644001.35 KB228e65bbb2986163fae76f27c57f046d0b3bc3f76cabd0f9f8dc65e6ad31460a
test/data/fastq/error_double_seq.fastq10064400669 Bytes14b7fdfed604a3eb005d03cbe11d419cdccf81426bf6de1930fc06bf934dbd14
test/data/fastq/error_long_qual.fastq10064400609 Bytes4649efbe152fcc28e1c39b2721ce52f147252a7ee0b55ceb22d535dae1277d48
test/data/fastq/error_no_qual.fastq10064400482 Bytes28b8205b4b3ed0d76ff1e2aec7ffffb0ca506cb99f057b4270ba37f7a5a51129
test/data/fastq/error_qual_null.fastq10064400610 Bytes72af9fe18e7f35688f717b685771f6da3fb1534d54f3af0437be97ecf4c617eb
test/data/fastq/error_qual_space.fastq10064400609 Bytes0156eb0603451e674f6c49416aa9842f6851d253f55a6765fb932960ce885f8f
test/data/fastq/error_trunc_at_qual.fastq10064400582 Bytes894945d96905c98e3e70d10b25e7ed702f151da44d4f4d56e7a479f30e844bd0
test/data/fastq/error_trunc_at_seq.fastq10064400522 Bytes445e7f307bb609c84a138a8b2e036aad4c9a8343029af9ac8ba3864aff7fe680
test/data/fastq/error_trunc_in_plus.fastq10064400562 Bytesc1993b571312617ae0acbc9226bcd616e3cee246c237e87be5c02148bf11ef29
test/data/fastq/error_trunc_in_qual.fastq10064400607 Bytes07e2bb6d586f5130181db31822e5c311413d99bdfca61aac376983b85144c953
test/data/fastq/error_trunc_in_seq.fastq10064400535 Bytes6e7bf90bde5e7b011d52b7b4c956734818b9a52fa04a34e978d3b405293b7fa0
test/data/fastq/error_trunc_in_title.fastq10064400513 Bytes15592000903ec62f12a22835bd0194e85b1c40ead8732c70e6f95e265c74db33
test/data/fastq/illumina_full_range_as_illumina.fastq10064400426 Bytesdc2cbaea780de049b285d2b13c0f9a7cb270f7e493a2233b9846060b56ca3e77
test/data/fastq/illumina_full_range_original_illumina.fastq10064400426 Bytesdc2cbaea780de049b285d2b13c0f9a7cb270f7e493a2233b9846060b56ca3e77
test/data/fastq/longreads_as_solexa.fastq100644008.19 KBa922d878e416ecc7df755f0e263dfe31078bebf298f1c85e6a5c980a6cc38bf5
test/data/fastq/misc_rna_as_sanger.fastq10064400774 Bytesb50686397fc812ecf7c726901acc1f127be1d29dcb6039bf35970e378ba51893
test/data/fastq/sanger_full_range_as_sanger.fastq10064400550 Bytesdaa8500ee0d0b8242c65991f4965b1ec445cf9f57565b838d3ba760e5313cb00
test/data/fastq/sanger_full_range_original_sanger.fastq10064400550 Bytesdaa8500ee0d0b8242c65991f4965b1ec445cf9f57565b838d3ba760e5313cb00
test/data/fastq/solexa_full_range_as_illumina.fastq10064400450 Bytescea9449b8602d7a29b6eaa45a0ecb2edd3e25cb3273f1476e05ffd3766da7cbb
test/data/fastq/solexa_full_range_original_solexa.fastq10064400450 Bytese6c95762306bf1cbfd7bb952215fc20751caf2448c083f6fdf4414dc8f96e8c1
test/data/gcg/pileup-aa.msf100644003.4 KB94a8f78752867af033bc76e9541f8a8a1e5ad2c52030364c6655bb3a8f1b7cb8
test/data/go/selected_component.ontology10064400553 Bytes7ca3d2f1c054079ebf3b61c1dd87af6a6a8b99c9f93662a6ee92151ca6997f6b
test/data/go/selected_gene_association.sgd100644001.79 KBa26eab8a1cc29bfbc972a4d64ac1ccc1e65c2bb01aa6a46c7830e7408793d3b5
test/data/go/selected_wikipedia2go10064400798 Bytes5715946c196b7b6ca89bafa343ee944358b6ae1e4ac51f2c284d50c4401f900b
test/data/meme/db100644000 Bytese3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
test/data/meme/mast.out10064400548 Bytes0b4335e26f7f1e3558443ed2d6c96e3f1403bda23599b41bfc54d403ad674222
test/data/paml/codeml/control_file.txt10064400409 Bytes1dea05cfccc9947e7730d1997d3a4ddb7be6c18792b4d09e6b56460420567366
test/data/paml/codeml/models/aa.ph10064400171 Bytes17aaa808426512c93af7eb5b80ca714de08d96112ea6a5512484b601763135be
test/data/paml/codeml/models/results0-3.txt1006440019.9 KBb7689667764422c4c0c118e245cd88d58519482eb92debdf445f53b5db5ac154
test/data/paml/codeml/rates100644007.41 KB613b284a3821ed6c1cc2f6f03db46b509cb045ac45763fe66e1ca7c0b15af081
test/data/pir/CRAB_ANAPL.pir10064400267 Bytesb7737f32f814f8f9cdae8b3759794e531ed2b731cc1661f6fe5c8e1c00ec0ef3
test/data/prosite/prosite.dat10064400167 KBcffe5a81263ac7e3877bab8f7d32e27ea722411b4d4f0fca235fe4e552fae671
test/data/sanger_chromatogram/test_chromatogram_abif.ab110064400223 KB8dcd2b30c70cc4ca455868b9f0df5dc588c54ff0be00066810c11442acd6effc
test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf1006440046.4 KBbc906663f3e6051bad5bd77d351c855991ce7dd4f68ba59909245aafe918153e
test/data/sim4/simple-A4.sim410064400661 Bytesab1a4c389192697f64269ca4af532edd7ee94977ef0ca5c64694bef727bb6768
test/functional/bio/sequence/test_output_embl.rb100644005.32 KBcc9df3add69492bc7de5a48d2bb12cc8ebf208c09d238e3204ef29e6af88c476
test/functional/bio/test_command.rb1006440010.2 KB8ae5128f5efbe7ef1844c4ea0728d60498484e8507d28f2eadfa05ddf43e840d
test/network/bio/appl/test_blast.rb100644001.33 KBec4f5912fde7b33acba042990b2b16d007bf69ef2cf3d7ca7dedb7225058e90d
test/network/bio/io/test_togows.rb100644006.82 KBe8064a6996e1be6350a97177caddafaf7dac159feb10015873fec43fc7125eed
test/unit/bio/appl/blast/test_ncbioptions.rb100644003.24 KB51bd4d197aec97dca14403d1771d7efa34146d8c7448fca6166908df9a505905
test/unit/bio/appl/blast/test_rpsblast.rb1006440014.1 KB126e813676404f765f502648cb0bf394f2232915e130ef38fee3312f636d1ea6
test/unit/bio/appl/hmmer/test_report.rb100644008.51 KB8388e84f4c6e92898daa0e3e186247d42022c4415d51a157685c36750c044bcd
test/unit/bio/appl/paml/codeml/test_rates.rb100644001.4 KBfe7b2055f05e01cfbb8cb01c6fea59fe5c2ec794fd8306f2cd6af9ecaa1c6e69
test/unit/bio/appl/paml/test_codeml.rb100644005.31 KB5e6bc2dd067a706f06ecab978dc95326f651fc46bd4ed3d4e84bcd1acdbf2793
test/unit/bio/appl/sim4/test_report.rb1006440022.1 KBa0c40c9d6dffc7148445102c188c7ba3b448441ad7d01c86982ec4037b01bd6d
test/unit/bio/appl/sosui/test_report.rb100644001.74 KB57a19935010147b937e38e14387d10175458e10e968f5f03a750dbccc0695f52
test/unit/bio/appl/test_fasta.rb100644003.16 KBf121d02629730c5fcd79783a6209b04dc2f0a4a179b07aa53a71c2eecfa74e34
test/unit/bio/appl/test_pts1.rb100644001.75 KB646eecf9f286f7eeed968357376f2ec18b2b6313bb6a7da7373f6a9ef94f5e31
test/unit/bio/data/test_aa.rb100644001.86 KB2c800117a296a02a2a23a4677c830dffc5fd5e0233d2d97fbaf43ef71fca5b92
test/unit/bio/data/test_codontable.rb100644002.43 KB5dd2fc71d0c7a7a96f8458437e622e6f140599dc570df2443f8cf3f9c3095837
test/unit/bio/db/embl/test_common.rb100644002.44 KB3a45afffa2256b1ac8f03787fada8e55638db074fe4b88d6e9e7263926e9d622
test/unit/bio/db/embl/test_embl.rb100644004.64 KBac18a4cd8b2c97a8d0efa9d9bd81a6ff94b207a2d60ccaa1cc638497746a0490
test/unit/bio/db/embl/test_embl_to_bioseq.rb100644006.03 KB1e318ccd79d77a1d122c0921449bbf9309a7ffe2e5e0091b01cf9445f0fc6779
test/unit/bio/db/genbank/test_common.rb100644009.47 KB607b53c849f08e83757153c462b893f39ac8e8570409db5cb27de98bab7ceb88
test/unit/bio/db/genbank/test_genbank.rb1006440025.1 KB6985ff8d2277b0695ec6ae38268ea18129fea92dea4e7bb5eb0b63e1d39ba8c8
test/unit/bio/db/kegg/test_enzyme.rb100644008.82 KB277729fc0a0ea3e384178904b93fefd49b070a2fb76af3a3f16385b7f140982a
test/unit/bio/db/kegg/test_pathway.rb1006440043.2 KB606f888b6f0324edd0406e862a2574702b690a8d8c5c776dd42cbd9dac9179e1
test/unit/bio/db/test_fastq.rb1006440030.4 KBa748c22b90bc28dde4bf82c58dff9a022a4df45a1a5a717ac650aa2b22b6b516
test/unit/bio/db/test_medline.rb100644008.72 KBff1f25de1fee160868cf3ef24ffc5194a7da49a98903d9d33955ff15d7adc3c4
test/unit/bio/db/test_nbrf.rb100644002.44 KB5d4b755a443113e6ab0fcfbe32e1f1d94edc111ec6f5604ec2be54a6a4aadf81
test/unit/bio/db/test_nexus.rb1006440015.8 KBb42c25aa6f0cad1c1adc2e96e3b1b81a186f945a29ac3a9e8d231f1f6ad1e5cc
test/unit/bio/db/test_rebase.rb100644002.5 KBba61c71f56f55add6307d6ed0aaf465153051394e17d1bb5abb03a246838c861
test/unit/bio/io/flatfile/test_splitter.rb100644009.31 KBdfbc875d39179539d42a05474f3bf74fb571fd78e8c220b6d223c82cd7ce4a73
test/unit/bio/io/test_fastacmd.rb10064400910 Bytesa9d74d969ae0ea1d960c30828fb7ce7e69990c77d64a416e8c01846a67cbc8f8
test/unit/bio/io/test_togows.rb100644004.33 KBc7baee90ade868c5803dd629d1dcc879279e8b1973a503490ca2127c99a6c55e
test/unit/bio/sequence/test_na.rb100644008.14 KBa27753afa3a74455f55cb09046a4784908677d8e5b953ebb86abbd2b134d267f
test/unit/bio/sequence/test_sequence_masker.rb100644004.72 KB9117e63f9f2bcc13ee0cdec24473315aea47b9af4fca1ac2077563551bd918e3
test/unit/bio/test_command.rb1006440011.2 KBe794d78475b19e588a953f29de60d509fe25dc772f6e11bb342ca152debff257
test/unit/bio/test_map.rb100644008.1 KB609d4551a3506a90e086c24b1daeff3a34762bca796640213f4aea7e5916586f
test/unit/bio/test_sequence.rb100644009.25 KB894f11db197b2455ca9acdd172e56ae2c1b046e6f29876c4aa80384b3203c3a5
test/unit/bio/test_tree.rb1006440027.8 KB8ecd584587bc21579399b9f9506a4c6988be1c601665b5e53acccded653749e7
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb100644002.16 KB57aec6958b4f00e82ee882aed1a49a1725bb14d96d33667a212ed90aeba6a4cc
test/unit/bio/util/test_color_scheme.rb10064400965 Bytesd214c1911f0a1c35e1b78e8c62be9642392077df2ad622ac354f1882d6b34758
test/unit/bio/util/test_contingency_table.rb100644002.92 KB88fad51c5b885925c3262c3d62975f7eb68d0f759773370c475cc83f84e31eda
test/unit/bio/util/test_sirna.rb100644006.15 KB98953b251ea93177d4d3471b2ffb36574d416cf79afc74ce5b2cfe390a3e692c