bio-1.4.0

https://rubygems.org

id: 11287

number: 1.4.0

platform: ruby

spec_sha256: 89c0f499a10e2a377cfb47532313c917767abbb6dae06e2dd2b8defd582838f9

sha256: d0406c03269a4136c764f34eb4e9706dae003ff9e51a71c72c3d9bd8edebe58c

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

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

position: 14

version_data_entries_count: 565

uploaded_at: 2009-12-29 08:51:56 UTC

indexed: true

has_extensions:

extensions:

Gem size: 1.21 MB

Version Data Entries

Total: 565

Unpacked size: 4.73 MB

Full Name	Mode	Size	SHA
test/data/fastq/error_qual_space.fastq	644	609 Bytes	0156eb0603451e674f6c49416aa9842f6851d253f55a6765fb932960ce885f8f
test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml	644	1.86 KB	2446e2a045b8648e528d9ee46deec710e9930b7bf17da2aaa063ec5a51ed5c67
test/data/meme/db	644	0 Bytes	e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
sample/any2fasta.rb	755	1.33 KB	2b781b7bdf098238d5fe0772f5cabeae4130d09755ba1c8f9fa05d9cd9338a32
lib/bio/appl/tcoffee.rb	644	1.46 KB	5d6065494772947211a2b8d1b5d50e84aae79c591238ba640f86fdce51a2b706
lib/bio/db/genbank/genbank.rb	644	4.09 KB	882fb7d27ca272b81e2853139510a58c41ac3ad44ae497790dbd8caa751590d1
test/data/fastq/misc_rna_as_solexa.fastq	644	774 Bytes	073dd9509de2be068bae20cae68c546727c8043de53298a3093afbffa9dda3f2
test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb	644	1.31 KB	900639ed4e1a581307b1dbdc126698024af756cf71b2077fdfea4542a47e7071
lib/bio/appl/tmhmm/report.rb	644	4.3 KB	35643d70c379494d510a253dc0cd1807e9cf9690b77730b639bb34bf25523806
test/unit/bio/db/test_prosite.rb	644	18 KB	b244e49a2fcd841894ec25a9ed3cacda768f61575863a44f2edde1f3ff94e921
RELEASE_NOTES.rdoc	644	6.1 KB	ef707a4ad5aae17a4fdaa99ba3d17b7c0b5181f44804008dc24380065a27a055
lib/bio/appl/blast/rpsblast.rb	644	8.87 KB	483485c64482118487c94d4ce43b79d1b670f485bb75cd79865c1bb50b25a419
lib/bio/util/color_scheme.rb	644	4.94 KB	a2e614c3205ad4e364eb422b703efe3184afe8261515565588406c4a17ecbc30
lib/bio/util/restriction_enzyme/range/sequence_range.rb	644	9.22 KB	c476ba4e8d13695c7aa1745ff91f39d2d938f246b900fec033a9e5b099456d8a
test/unit/bio/db/test_newick.rb	644	9.45 KB	941e81242f77bbc357bf45f27da0e23800b212b06aa17780c479110066763c17
test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq	644	984 Bytes	7f6e883493ac3be2114dfe4794e4a324bb67e7e9064c211bed60a6527c783b33
LEGAL	644	4.41 KB	5260182d652bef11239763707e13a8c23e06b5d9f8610d60c75ebe7fe9aae36d
doc/Changes-0.7.rd	644	12.8 KB	dc32dba9fc065d700458cedbb493c30ca341afcd4541e53ad81b956cb8ee2263
lib/bio/appl/paml/yn00/report.rb	644	644 Bytes	bd7d8221c4272671781bf8f07a4405f30bb0b1ac804c0077da34cdb361678fff
lib/bio/appl/pts1.rb	644	6.07 KB	4d4915e5355ac18703ee51cc9fd55d9cd9721019acb425bf45da1d930c70c43a
lib/bio/db/aaindex.rb	644	6.78 KB	3a2dfc2c82ec4b9108f72f1a0f44f1dfab62681123e6206408271c1cd08820fe
lib/bio/db/lasergene.rb	644	8.81 KB	ab810df2b17490d5b9e55de9e96999ccb14ca3d2e8bb19614a8ff34f169d1f44
lib/bio/db/nexus.rb	644	54.9 KB	4a47cf0f5fa085fc5e51402a65c18690de99304efd0364a68795936fab7fda4e
lib/bio/db/pdb.rb	644	594 Bytes	75fb017faf8c188ceb846336c581b5455cffe63c4cc6ff6d3e26e264a1d3325c
lib/bio/db/transfac.rb	644	5.89 KB	9517ff987b3420e897fdc690f233ceb3cd9734257ecb33a2b4ebd9fb2d3a1008
lib/bio/io/biosql/biosql.rb	644	1.86 KB	c29f8a0148670bdf1ffddce08bcb3fba49cc6dc759b74f387fdd4159f81612e1
lib/bio/sequence/dblink.rb	644	1.28 KB	772cf05b299a463368c70cb9775acd334b3223844869252d610958a4e243f423
lib/bio/sequence/quality_score.rb	644	5.78 KB	a8649c9f40a30f0126d20a9ae756bdbb5127f1df6527f65d68deaf8012f267b4
lib/bio/shell/plugin/soap.rb	644	2.08 KB	5d80fec34e0b50136894d5c96f14d44700ebd2b64ca9830cf37fe1ae99d6bd8d
lib/bio/util/restriction_enzyme/enzymes.yaml	644	87.5 KB	56ed1fd2f2d5557604da2044f3d491ccc5b845c43b4b307b395fb89e3798b346
lib/bio/util/sirna.rb	644	6.87 KB	ec19201ad6476dd6bd251a240afe4430603ecdb6a3f54f18bf8700d170b1d7b7
sample/demo_kegg_glycan.rb	644	1.5 KB	7716f364760283313fcd39d9b86f34ba6dafed0799855657cc834982b3316f32
sample/demo_psort_report.rb	644	1.42 KB	2ed41494c85b0f89a81c42c485740ec1220c0e2a82618a2c42365a5dd6c59141
test/data/aaindex/DAYM780301	644	2.04 KB	20b2940e4d45f6b2710ca0295998804233dd8407f607a8803dd428fdf82a55da
test/data/fastq/error_trunc_at_seq.fastq	644	522 Bytes	445e7f307bb609c84a138a8b2e036aad4c9a8343029af9ac8ba3864aff7fe680
test/data/phyloxml/made_up.xml	644	5.87 KB	232f5f075b0f7dc9bbe512f18bfc1cdf72f6380edc0343c90a68a8699e3dd463
test/unit/bio/appl/mafft/test_report.rb	644	1.97 KB	714147bf14490dd7197cf4596afbdb4d22922bb2d517ed6232e7e4a0fc399cd1
test/unit/bio/appl/test_blast.rb	644	7.11 KB	24425d7fe90d041804cca346a4d6a014c7e7b06cf262b8e857eb5a80daf4481b
test/unit/bio/db/embl/test_embl.rb	644	4.78 KB	d2ceb9c483f65cade7d48abb5ec22fcc268622e1f2fb90a482d1ac322449be93
test/unit/bio/db/embl/test_embl_to_bioseq.rb	644	6.03 KB	1e318ccd79d77a1d122c0921449bbf9309a7ffe2e5e0091b01cf9445f0fc6779
test/unit/bio/db/kegg/test_drug.rb	644	6 KB	f3c2bbd484c580a691006b0fab46a53847b73965a78b0f496dadc16f043e1211
test/unit/bio/db/kegg/test_enzyme.rb	644	8.82 KB	277729fc0a0ea3e384178904b93fefd49b070a2fb76af3a3f16385b7f140982a
test/unit/bio/db/test_fasta.rb	644	7.54 KB	8c2edadafe6a4108b989db31f8a3381bc077ac99611bc4395b4c747406c11b48
test/unit/bio/sequence/test_dblink.rb	644	1.64 KB	76fd4a775401443ca5da30ecab704e5565726aa78e23456935582575faa4dc39
test/unit/bio/util/test_color_scheme.rb	644	965 Bytes	d214c1911f0a1c35e1b78e8c62be9642392077df2ad622ac354f1882d6b34758
test/data/sim4/simple2-A4.sim4	644	672 Bytes	dce2c8000b726b2ead80fae52e4765da3572e174534e691e919d38d9787fd301
test/data/fastq/error_trunc_in_plus.fastq	644	562 Bytes	c1993b571312617ae0acbc9226bcd616e3cee246c237e87be5c02148bf11ef29
lib/bio/location.rb	644	25.5 KB	82489e9536af49b99fe131064dad40503c12571a01968cd388d604c1cc87fad3
sample/fsplit.rb	755	1.11 KB	400c70b8905f27f74fd581c8c9accf5ab24748c9725131890d3e8a560dd4b80b
test/unit/bio/util/test_contingency_table.rb	644	2.89 KB	6936d48361c8868a0a19a6d33a9afffe0e42796a76046ed52a4efb460928dcc3
lib/bio/db/fasta/qual.rb	644	2.52 KB	885960e201b24f7f39a699b25f26c34db3b0fe45673153bc4b183306748f693e
test/data/soft/GDS100_partial.soft	755	4.41 KB	1bfefad740153929f2e57e33eb45487558e52da5e577f6a1c690c06f7af5ed0b
lib/bio/appl/hmmer.rb	644	2.07 KB	1e017eb253ba728e6f46226e8e4720da003a8fe6b994c51ccd506913c50bf9d3
lib/bio/appl/mafft/report.rb	644	6.51 KB	1d4b4cfee1e66e52d7c39cb7f3086148d38b815d44f843f33a30d4042e42db33
lib/bio/appl/meme/mast/report.rb	644	2.47 KB	b1332d1e715afb8011b420e5ff70beac7e450381913fd260621cad9cacf56ef2
lib/bio/appl/paml/common_report.rb	644	844 Bytes	a6bf1e607f9d94f754900c1e5d14d1a42dbaf70b9f123ef8f37cefd5bcef7163
lib/bio/util/restriction_enzyme.rb	644	7.9 KB	b43029ea4aec25a8a87e8a43ab204a0193a60ed29551f0ee20221b93d3a95dad
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb	644	2.9 KB	1fcd5f98ac571a6af6a1a13c4d74dc9eddd524454edd2d5b1c7f98ab858c4ae8
sample/ssearch2tab.rb	755	2.24 KB	f48f03ed7e929175411bdb75df185c16b906a9fd5fc0f3e7c8feb1a95536a25a
test/data/blast/b0002.faa.m7	644	5.52 KB	bb7d1c37f92f8a36527c02efb6f6352294eb1acf688ea6caedb7b934f9817e8f
test/data/fastq/error_no_qual.fastq	644	482 Bytes	28b8205b4b3ed0d76ff1e2aec7ffffb0ca506cb99f057b4270ba37f7a5a51129
test/data/fastq/illumina_full_range_as_illumina.fastq	644	426 Bytes	dc2cbaea780de049b285d2b13c0f9a7cb270f7e493a2233b9846060b56ca3e77
test/data/fastq/longreads_as_solexa.fastq	644	8.19 KB	a922d878e416ecc7df755f0e263dfe31078bebf298f1c85e6a5c980a6cc38bf5
test/data/genscan/sample.report	644	2.7 KB	f13ec60b9b006881654cb13344f92618f94d669cfa2fde890be41f37f3f38ad8
test/unit/bio/db/biosql/tc_biosql.rb	644	4.78 KB	c51a501d98932e2e22fbf001c7a7ad7a65b8441dbf59238117fa41e1d90d9c51
test/unit/bio/db/kegg/test_genes.rb	644	1.76 KB	aeacefc32e7493c526f3bd47845eef28c8faf52e2f6fb1cb2a7ce18c487e7a90
doc/KEGG_API.rd	644	56.5 KB	9ee195347052b4665f91cf571c25fec39c8dad7dddad756cd158914277cdc8f9
lib/bio/db/kegg/glycan.rb	644	3.02 KB	de0c9aabcc82cc881f0c3bec1245207f1e5786866fc0b80f463d16ec9332c528
test/data/fastq/wrapping_as_solexa.fastq	644	963 Bytes	73211e22ce6ce16d579f3ee1a2dc0eec913e20799185655305bbbd7670364811
sample/gbtab2mysql.rb	755	3.99 KB	92b5b3f0f9ab26f44e193bd51adca9ad1c41dbbeff05cf7395cfc02d40fd8624
sample/genome2rb.rb	755	910 Bytes	c163eac8c0477dd2b7f93400518da3f656d11de834693f82c432add97876cb06
sample/na2aa.rb	755	990 Bytes	5d4636fcfba5ba91d2c7f50e48b3d3c7ca4eb811238ac6578909c933a2572ae3
test/data/KEGG/K02338.orthology	644	27.8 KB	928ce72b385e9be6baa56d14f0acae9b5af46bb10adcd9cf7735d217a5f2fe1a
test/data/fastq/misc_dna_as_solexa.fastq	644	767 Bytes	5323e24d25cf1ca763dd002553a80424c4e4e2011bd677eb60ba05ea3d7c410d
test/data/meme/mast.out	644	548 Bytes	0b4335e26f7f1e3558443ed2d6c96e3f1403bda23599b41bfc54d403ad674222
test/unit/bio/db/embl/test_common.rb	644	2.44 KB	3a45afffa2256b1ac8f03787fada8e55638db074fe4b88d6e9e7263926e9d622
test/unit/bio/db/kegg/test_orthology.rb	644	1.34 KB	c58c3d1f74b75bee7f907af4bcafb6f6f35958d9c378165d5b0483ebf5e9fc26
test/unit/bio/db/test_medline.rb	644	4.39 KB	adf49ea34e1cbb026120e57cc8c7eede4f76794c3da804aad2d4b36319f6a1ff
test/unit/bio/io/test_fastacmd.rb	644	910 Bytes	a9d74d969ae0ea1d960c30828fb7ce7e69990c77d64a416e8c01846a67cbc8f8
test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb	644	5.07 KB	f8fb8b389728d100a83117ef13cc8f1786a809ee9a0b96454f0cc86f333496de
lib/bio/pathway.rb	644	22.1 KB	7ff5a3029518260fca6522517a510928bc1be747491fff8461aaeac9fec59855
test/unit/bio/io/test_soapwsdl.rb	644	756 Bytes	639c4e9c1b295ff140b817a40eca991fc5c8c8ac7fd263c127606c714365f966
Rakefile	644	3.81 KB	d343576650f2ed5b5d169aec464bea75cf965a6bf3893132a161380cdd26c0ab
bin/bioruby	755	979 Bytes	bbe0535bab46e968088196c828fe6700e289594fbf124ae16f0db556d14d882b
lib/bio/db/embl/embl.rb	644	10.9 KB	dc30f672b12b23c13f23621732cd46f08f41905b99e2978c0a20512ad3dce7e5
lib/bio/db/pdb/atom.rb	644	1.7 KB	62476bbd1df9808017c5728cc4d18d2a492ed6e89c74196dcf41a4a85c94265e
lib/bio/io/fastacmd.rb	644	4.1 KB	fbbc315bd926712bf1e78e5acbb31beac08f4550fe05277a6bece94db822e2c8
lib/bio/io/registry.rb	644	7.38 KB	9548f9c05e41bc653b1c149f484a174dae94346cc02fa1564deb9215a576f9a0
test/data/blast/b0002.faa.m8	644	56 Bytes	6c329cdca78f16508223e98bcbe25cb26e96d8e24180439e1ca913034fd261e6
test/unit/bio/appl/blast/test_rpsblast.rb	644	14.1 KB	453a2cc370ff7f20f3c679fec6cb5ed4f96213f32cf06a08a0e69ae294d07ab2
test/unit/bio/sequence/test_compat.rb	644	1.68 KB	755f9dc47663fa487cca44bf74af2398d35f371e52f3688b4deb2b708cc6cf6f
bin/br_biogetseq.rb	755	799 Bytes	2ceea85a863d416213b4d4e1aebdb53cfbf3a6fd84fdb9f36c7a50a85bb32a60
doc/KEGG_API.rd.ja	644	54.5 KB	b8393f5e262b31e2acc94b1eda50eeba2d69ee7f4d8c9a9857680b95148fb243
doc/Tutorial.rd.ja.html	644	98 KB	58fd4eb3bfbdcd4797b767ff61d8b546588116666233a3e885c2b9bbd6b1fe90
extconf.rb	644	42 Bytes	f7e2d00da8d1364f842b3ca91d711ec3f63f2208dc4a9541c6518e2055b8348c
lib/bio/appl/sosui/report.rb	644	2.24 KB	59593d84abe70374d5f7f4afb13bf967534eb87ce7a6c423ddb3bc387ae99a79
lib/bio/compat/features.rb	644	4.5 KB	8a247d12e629ed46fc4e7f11f632b8e7f9cfae9b98a8af18e3a7c2d999d815a6
lib/bio/db/biosql/biosql_to_biosequence.rb	644	1.7 KB	ba9c18d2ea1def2d2b7982c64a7d65188df0b62ae932d1f4b975929d9b6e227d
lib/bio/db/embl/swissprot.rb	644	1014 Bytes	a48b17fc793812516ddf692232b14e62e0f87bd8a9dfe3a5631eda69a5848ae3
lib/bio/db/kegg/common.rb	644	3.05 KB	e3c49d9c3c048a600f38b948872dae214109fc1019cbbdffa039daf5c95c2c18
lib/bio/db/kegg/genes.rb	644	8.17 KB	8b721e257601095250a3f151eb61cf2b5f379f4f6b7bef33c085a242880f869b
lib/bio/db/kegg/genome.rb	644	5.01 KB	2482ac12607bfe4e69e14252a7181b9a28e338c5063b63ca75ba3db20d8d6c3b
lib/bio/db/pdb/utils.rb	644	10.1 KB	83cb0adebb7e7bec06b425f627e3b05d9df562b76ca24b9451a6441e0e99bd42
lib/bio/db/phyloxml/phyloxml_writer.rb	644	6.5 KB	8dc79a0bc8755bc91b308b31feb2337137b741055f8265e492f635f7f23677b8
lib/bio/db/rebase.rb	644	13.8 KB	d5913b0ba399fcf4f694e7efab6be6aa09ef5b2c449be4ec2b1c165bcfae7ebe
lib/bio/io/flatfile/autodetection.rb	644	16.1 KB	cf65edbfdf700cce5bcee2a998b5b24783769bd10a2bdb1ebcaaf35c807f896f
lib/bio/io/keggapi.rb	644	10 KB	f5aa0995d597117e19122357afdc7a3625d889cbe07402eee075f77cbfb35466
lib/bio/shell/plugin/das.rb	644	1.01 KB	65258848a7b0c1e90740cdfd8235c478c92ac1a434b19255c38abd2544abed05
lib/bio/shell/plugin/keggapi.rb	644	4.76 KB	d57e48fcc23204e607171447424ecd3075768acd171cc87ed1b99510cf934b6c
lib/bio/shell/plugin/midi.rb	644	9.85 KB	b3e1173d5009c7df0ae5bd06560292b4397b26c7a3b06c7f3639ffc1bd4ea007
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png	644	6.79 KB	483e2f19ce8966c8490191c261d40e3bafcff790c1abdf21060307e31ef2372d
lib/bio/util/restriction_enzyme/range/cut_range.rb	644	593 Bytes	cd3c8ec45c3405bc00eb6359e8cfae4d83b8153759b1e1496fe3b0c50a2bf97d
lib/bio/util/restriction_enzyme/single_strand.rb	644	6.62 KB	68d63e357dbced77555563e5a043942d9e4e3a78ffe48b6b11fde80308065135
lib/bio/util/restriction_enzyme/string_formatting.rb	644	2.83 KB	222f84fb60277208e57b30341fa3f7ba2867ea461c01aeff4c1b001d6cc4bc8d
sample/demo_fasta_remote.rb	644	1.14 KB	d3333a88bd43f07419197e1e93621cf95cf7a8683738da3da4c54740250a817d
sample/demo_genscan_report.rb	644	6.05 KB	3c4587e3a6e4bc54c8508e35daa374152e1871687fdf1d80823c78a81fc8cb6d
sample/demo_hmmer_report.rb	644	3.72 KB	e59b19e3d17c68adaae6d0e7d432531310cad2b1bc074e8d593bed378f3bb5a8
lib/bio/appl/phylip/alignment.rb	644	3.36 KB	74ab9a941fc46def4555c416d5502eaf884d8fe7da4499b14a57df98c5d15ec2
lib/bio/db/embl/sptr.rb	644	34.8 KB	45b92e71ce83d9d5913eb1211f3351fef1d1b9b4364ccaa8e64f78a1509b8126
lib/bio/io/ebisoap.rb	644	2.95 KB	fb8eacdbc9778a088eab23bcd721946bc46c8780ade929f1927765cb4a59393e
COPYING	644	2.45 KB	d18b5463859ebbe78e33e13bf7a6241d4d69a7c484f677d7aea7f8bbac039531
lib/bio/db/genbank/common.rb	644	7.49 KB	7675a42bf17ca546b5b7bddcba14002a5af7d1aa6f7878beffb681cb5031cc9c
lib/bio/db/pdb/chain.rb	644	5.58 KB	78e500a2b9a6ac23cd70cd3909fe4a2b56f047cd8315b827bb599ecd68f704d5
sample/demo_kegg_genome.rb	644	1.44 KB	f929c3029ba2de4487f047221a1059c43c972467687be02683e250ceac6d2255
lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb	644	803 Bytes	4a22c7c7063b42ca96f2809acae97ace54e65ac5ea93d7160ccff2c3bef7dc73
lib/bio/io/flatfile/bdb.rb	644	5.55 KB	a0151a2360d3e2a0604e37b78830c26c9da2f84a29d89015476e35a525a7d26e
lib/bio/sequence/format.rb	644	10 KB	afc727690585fe7da68f0f3758b301e99d81fa9f330770c601feb42edc3a7f39
lib/bio/shell/core.rb	644	12.6 KB	d1664b180dfdb34a7ba30ed62cfdcfed288ba17c58e58e007943a34c1a1120aa
lib/bio/shell/plugin/blast.rb	644	789 Bytes	363a9cd26d862b6fc7d7dd6cba92eb1e5f8a1e85252768e14f22ba6691b141d8
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml	644	142 Bytes	f636303863e9caae6ad5b285d102c3b2f8451353c15d3163f7333e5c10512141
lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb	644	1.79 KB	09e37d064b972eb2495cc4e490b0b7abe045b18317c4fa93d7b5676c19faa328
lib/bio/util/restriction_enzyme/single_strand_complement.rb	644	730 Bytes	47d32c263f36934713f03c1d70d8f2fa0006a326c70bf7ff645eb65071d99cf1
sample/color_scheme_na.rb	644	2.01 KB	8a184ec205da562d16d8f1b81ed89ca7ee61d44b1c29bcb104d3d3baad4fdf1e
sample/demo_prosite.rb	644	2.12 KB	b5d1ad86818fcd67e730037829d480ac976f1c4cfdb64420d67cd481809e0ac2
sample/demo_psort.rb	644	3.37 KB	d399f80d7e1919ca8189c90a6ee7b4299ac90a4a92c19f21b3357b214af0baaf
sample/genes2tab.rb	755	1.73 KB	4d160b473fd20374635ca2a04130913b0c02ed3b94169785727f88c13d14b5aa
sample/genome2tab.rb	755	1.65 KB	5325f258867cc7f73710c9773bde73c12dbce2e4edbb3e2e8bc91c887cf06ad3
test/bioruby_test_helper.rb	644	1.68 KB	3f608857cec3682f90d1dd045c7d9d651e37907eb86a720728251253e6d11493
test/data/KEGG/G00024.glycan	644	2.32 KB	203ec01248d66a18e40a046c9f30c0a4bcd2a124cdd40599a29c785280c78c2e
test/data/TMHMM/sample.report	644	909 Bytes	9f86ea10faa13634881100b73613287672f62c509903768c33ac1d4d4cda4b4c
test/data/aaindex/PRAM900102	644	1.08 KB	62991a1bd9b197111da30dd3bd8f2a637c435778aef8d2bbb548c5e0fa8ea69d
test/data/fastq/error_double_qual.fastq	644	669 Bytes	bcd0f39312b6629a9bcbf5e260bd99f2edddd27ecb77df91bdeeda1bb7d351c0
test/data/fastq/error_qual_tab.fastq	644	609 Bytes	c2a85269fc0b2f6b0b8dc02d6026b583b82638fcc8e76f2888bbcef1da57f015
test/data/fastq/error_tabs.fastq	644	629 Bytes	bcf82ae47fca310a4ab418438f6158d47e9e93d5a4b8d0258230c58f15674301
test/data/fastq/error_trunc_at_plus.fastq	644	548 Bytes	785fe4189c44bb5503b51a9e26ac58127cfb8cdea2ebe244213d2bf5deae7b0d
test/data/fastq/error_trunc_in_qual.fastq	644	607 Bytes	07e2bb6d586f5130181db31822e5c311413d99bdfca61aac376983b85144c953
test/data/fastq/misc_rna_as_sanger.fastq	644	774 Bytes	b50686397fc812ecf7c726901acc1f127be1d29dcb6039bf35970e378ba51893
test/data/fastq/sanger_full_range_as_illumina.fastq	644	550 Bytes	dfd416a2f4bfe648e968c915f322e98123eaf13cc7c3bd4344323471cf01ddde
test/data/paml/codeml/control_file.txt	644	409 Bytes	1dea05cfccc9947e7730d1997d3a4ddb7be6c18792b4d09e6b56460420567366
test/data/phyloxml/bcl_2.xml	644	105 KB	677e9a0520f5f260f41c31fe69946eab6ac30c924a4ceb9e97ed0b82825c7061
test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf	644	46.4 KB	bc906663f3e6051bad5bd77d351c855991ce7dd4f68ba59909245aafe918153e
test/unit/bio/appl/blast/test_ncbioptions.rb	644	3.24 KB	51bd4d197aec97dca14403d1771d7efa34146d8c7448fca6166908df9a505905
test/unit/bio/appl/meme/test_mast.rb	644	2.75 KB	853e762224db2d84f48178ab9dd23ff9f3b43079f0c927c2a7e353e3ce8407cb
test/unit/bio/appl/tmhmm/test_report.rb	644	3.2 KB	58ff701c8d1aacc023648e8acfd3c13698b82d77097ab212158b2ef529de792d
test/unit/bio/db/test_phyloxml_writer.rb	644	10.2 KB	cfc7f830f8f39c124dc1f895429a46bd8d1da3c87e039c73b04e0587005694a6
test/unit/bio/test_pathway.rb	644	14.3 KB	9b55cf2a8df75f327ea80f4d35a181d60384d739a98b3808b12f9d8e66aa7091
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb	644	1.47 KB	bf40d893499726b091be88692cbb7a7072503cba1528527f34d0c2fc5fd7cbc8
test/unit/bio/util/restriction_enzyme/test_double_stranded.rb	644	3.83 KB	8e71d644dac4188ac4e3a6a850af252febfafcff1f0c2e627865369033729424
LGPL	644	25.8 KB	a190dc9c8043755d90f8b0a75fa66b9e42d4af4c980bf5ddc633f0124db3cee7
lib/bio/shell/web.rb	644	2.18 KB	2075a224e814a0e8dd336dbaf323a7e3a3b8a0e49fbca169e8221a0c229ae123
GPL	644	17.6 KB	204d8eff92f95aac4df6c8122bc1505f468f3a901e5a4cc08940e0ede1938994
doc/Tutorial.rd.html	644	50.5 KB	1336e645505612c6eae93d1b2c7253c0142c878dffc67175572426bff390930f
lib/bio/appl/blast/rexml.rb	644	4.14 KB	bfd93b105ccd8608df03e69076b80165ef72b4c7578922a779c3071ad364bf0f
lib/bio/db/kegg/drug.rb	644	2.74 KB	b5ef401b465659835991cb1658f078cd9d84b72a7efa7ff029d404919078b7e7
lib/bio/shell/irb.rb	644	2.28 KB	5ea436be30792395277b73e63b4a313a8019bf6dc3c488cdb1c0f36f43f66ab5
lib/bio/util/color_scheme/zappo.rb	644	1.07 KB	4fbe84b2835206f44f0cf7ad95889c7c28f4a207ed015f86436dd5e47f534ce5
sample/demo_ddbjxml.rb	644	5.37 KB	e328c5e621c4b9065c905cde8a0c72d0d5941b2866851838119ec5953ae016bb
sample/demo_gff1.rb	644	1.18 KB	971afdd41ea7679d9cbfe7ffc1491a4d8d75e71cb0926471eee54e11e3f1bb85
sample/demo_litdb.rb	644	832 Bytes	52bc6ee01104e8a5785ce9ebe94ccee7d341fa7f79b90bcde433a82cc27e4665
sample/demo_pathway.rb	644	4.75 KB	1ae00d528835caa4fc328830982ffdbf9aa90537a18862dc4a692dbf6c579833
sample/demo_sirna.rb	644	1.37 KB	4aac4578346e1a643757c55e1a30f0a3e1b891725d5225a5365ea82665e290d3
sample/gb2fasta.rb	755	924 Bytes	c41ea6c950dcc6d8295e292f7213b8460d71f9f7819e6e02a688ef350e270dcf
sample/gb2tab.rb	755	5.65 KB	bc7816d5b592ec40701d58978e0c94ffbdf63156a502c685be78ed54abdb0d0e
sample/psortplot_html.rb	644	4.95 KB	75a7811ea4d6aa05206b50aaea0643dc7d2d9b3813955d1d84904f227a9ceafb
sample/tdiary.rb	644	4.63 KB	7e6c6074a6486cdb0d1022f17f4dccc32d3ff0491457e0bd2a9e5e015b788272
setup.rb	644	35.6 KB	f011e968de24e5d9050895f278bd2946cb7d98ecc2ac4e9ea2cbf2cba80b03b9
test/data/KEGG/1.1.1.1.enzyme	644	42 KB	3abaef4380391a3bde08232e79074e336d1d29d78f3c8185f8b1dc11e7790226
test/data/blast/blastp-multi.m7	644	11 KB	c99e14d4bcb868f03515051dd8c0c32da98f580e22b9212425b6c775d6b8fa06
test/data/phyloxml/apaf.xml	644	37.7 KB	9e30420e948d58bc99863df7dafd544aa4137c277a7e02cd3e8a3e47adc9f847
test/data/soft/GSE3457_family_partial.soft	755	45.5 KB	dbb03aadc6b6db0a5a80b05b6b09ace4725fbdbd2862c6925d0a7c72b68aaef3
test/functional/bio/appl/test_pts1.rb	644	2.43 KB	5344321f243479c9202184d8e93edeeeb35c61153ec79332bfc8726b8a646a55
test/functional/bio/io/test_pubmed.rb	644	3.74 KB	5813b92453cfef93ab75f0844013d8e654e86f5835245325679ba7f8071d3761
test/functional/bio/io/test_soapwsdl.rb	644	1.03 KB	c33b7939624b2b8f57b4742613d1c7973320e2fd99432a7190e7710f234fd687
test/unit/bio/appl/paml/codeml/test_rates.rb	644	1.36 KB	e3b37afb2c9b7f9df8da20be9ae07eb04103cda0ba8ddefd4b0bd3f840bb3cfd
test/unit/bio/appl/sosui/test_report.rb	644	1.74 KB	57a19935010147b937e38e14387d10175458e10e968f5f03a750dbccc0695f52
test/unit/bio/db/test_gff.rb	644	43.5 KB	e570e2e66b673ab91e5c1cc4e125e08c006f2b7209c0ecde7ee5e9eed08bcad9
test/unit/bio/db/test_nexus.rb	644	15.8 KB	b42c25aa6f0cad1c1adc2e96e3b1b81a186f945a29ac3a9e8d231f1f6ad1e5cc
test/unit/bio/io/flatfile/test_buffer.rb	644	6.47 KB	6da483c552a90d32925eac6427089c376c1d4e7876839452c0a29710cc8f1e1f
test/unit/bio/io/flatfile/test_splitter.rb	644	9.31 KB	1fb08d95d65981a1d8ce3e7cce2c49376696cfca5ef40f6d3f25f3bee6b987ff
test/unit/bio/io/test_togows.rb	644	4.25 KB	b8c24ed5c5d252734ff423b105ad7666d6eb5dffb275c9c19fb1dfe49b2d291c
test/unit/bio/test_shell.rb	644	461 Bytes	854ea2dd1413610f58f6edefacbeecb68227a3268746128b7c1b1d2062ad3a4d
test/unit/bio/util/restriction_enzyme/test_analysis.rb	644	8.81 KB	00bb1a18e1a7a7e09c43eed2cd7cbd51d704e8de443de2f9dae8d4bde9ff8fda
bin/br_biofetch.rb	755	1.23 KB	c851dd31e33f68abf5d8af990db7e30ecb9c06af47a66034743e57784972a067
lib/bio/appl/probcons.rb	644	1.16 KB	f8899e8ac6e99ecf62a793507c2e51c4be2fb3a69f0c44e02bec869a9e3fb867
lib/bio/db/genbank/ddbj.rb	644	423 Bytes	1e206a3f3f93eab293fd6533debae45d4c7575dfe1edda71f81f76846abcd036
lib/bio/db/kegg/expression.rb	644	2.98 KB	8f4213871035a65826092c39a47a5f0302e57fe9a9e296f056faf76c3027023d
lib/bio/io/soapwsdl.rb	644	2.3 KB	a986284bdf999c960ba417a7ce244c8d8cfcd22faa60b1ca333c03fb0dca2550
test/data/SOSUI/sample.report	644	414 Bytes	1925c1a9a14b535fcdbc76c4e57ac1195a9f830c63345423ee426def973aa333
test/unit/bio/db/biosql/ts_suite_biosql.rb	644	194 Bytes	20f74925ce67a8da79e4cf65fea22495b22a3aea578121e1032b4b813f275596
test/unit/bio/io/test_ensembl.rb	644	2.42 KB	e647416048e81ed635f1e57c60d35cedd8429c129aac849440f416f1c724d395
bin/br_bioflat.rb	755	7.17 KB	8d87c3730fe70eac916f8915b9472fde9ccace80208b0e01cda83f66d7780199
lib/bio/util/restriction_enzyme/analysis.rb	644	9.58 KB	ce30016b52ee7520e2cba5d83363c057a72a664c84f9a42a6fb2dd2a9fcb596f
lib/bio/shell/demo.rb	644	4.9 KB	4f3a431e2485bdd19137a38e19ba5fa894c931f82b005083608c4f06e6629af3
bioruby.gemspec	644	23.8 KB	b1682d8300303d0034e8080d0fcdbf953c451e96530504590242ac0ecb8f9b70
doc/Changes-1.3.rdoc	644	9.46 KB	804d1a8e27eba9db6f0a53589bcd3613245c841d1248319afe36412b66f394b9
lib/bio/appl/blast/xmlparser.rb	644	6.79 KB	13d8d60081ef3ee391ec2efd47855b444fb0f7bda690c8444a5c7e774357ee78
lib/bio/appl/paml/baseml/report.rb	644	660 Bytes	9a4c272ea61596c13451459b6dcf3b386a3149ca20f972bd1b2ac0177ab82734
lib/bio/command.rb	644	19 KB	ccbdc39375cabb54dc8987caeb6db8eb0269f8c9d35500fbfe8894f796b6ed9f
lib/bio/db/genbank/format_genbank.rb	644	5.35 KB	acd8c06f5d672b14c7c948507b5f61e5c79c52408e3c22e46b2ab7c724e11e61
lib/bio/db/litdb.rb	644	1.44 KB	87e1716604ee85e915b579384dfc1cb8b9038bd94f4528e80e4bd18c1835fbb8
lib/bio/db/pdb/residue.rb	644	4.16 KB	8d7e598249f290913801d1957459e2f307cd39d72f8619775610d13f7d086d67
lib/bio/db/sanger_chromatogram/scf.rb	644	7.39 KB	f8fb3148e3110577eecd8852635f0a9d4da9b8117f0cc7c9a833ef1d3eb9b4f5
lib/bio/shell/plugin/psort.rb	644	1.17 KB	ab085742b7659066c313a6fcfc4c1b063233c173a18f97167add22669cfc0cfe
lib/bio/shell/plugin/seq.rb	644	6.53 KB	5c21f7ae85dbda5c18c954a9ac27980659b02d7cd27020f78ba3814e2a50d232
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml	644	188 Bytes	160318fc0d3ea31644ec64a11ff9edf0e60f66fe20c1f15c2d703c0252596555
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif	644	1.4 KB	cb34983afbbf48685f0848c55692ed18b7fcfb20d92a7d65447bd9f75673ebbf
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb	644	1.13 KB	becf3bf68fa08f81e54b9bbe60f241b1dc0e6a5d316480f6f477f4f7bdbf9dff
lib/bio/util/restriction_enzyme/double_stranded.rb	644	10.6 KB	5d70feb8d68c4580c82efc1582d9084ce5ce5c35d6832753b579f4807e7518ca
sample/demo_kegg_compound.rb	644	1.24 KB	e9dc8cc8a04054bcc59f1b07f479771dc26ec51fd0aa8f264299655d04957f20
sample/pmfetch.rb	755	1.35 KB	d5384d2b53695c0f2d2b15071fcf6d618c6d1c95baf1be7f16af09e14295b500
test/data/HMMER/hmmpfam.out	644	3.13 KB	e832f4b86eebeb3d956ca1ecef073986f108f22553916975a061b49d61c55c02
test/data/blast/2.2.15.blastp.m7	644	67.2 KB	723f8d684b11de6b01630896e6e96b37d95dc80344bf550128bf27b59200cb8b
test/data/blast/b0002.faa.m0	644	5.15 KB	2479b6f0b728c354edbf01fe600cd7884308e1e6a22913a7420e23af75cbfd75
test/data/fastq/error_qual_unit_sep.fastq	644	608 Bytes	a819e7f2a4d33695eb1916112d4ca95ab16bd58f7fcf1ef4798d854b59ceeae3
test/data/fastq/wrapping_as_sanger.fastq	644	963 Bytes	f8272a035e8908a7939f525de403563f726b577e37bae419aae8de55bc4502c0
test/data/phyloxml/phyloxml_examples.xml	644	14.6 KB	ae0f0f333d9553d8fc51d5882e73451a7796b4648b96668a145f1e6e4e16ed83
test/unit/bio/appl/iprscan/test_report.rb	644	9.07 KB	95723d81f560ab7570ebfa9557138a5b4968d82de19b5c6cb19447782243bb8a
test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb	644	3.32 KB	639fc408259b657962683068b3f09041214c930ce289e4aa1f43e5ccae0f5b44
test/unit/bio/util/test_sirna.rb	644	6.15 KB	9ba9f1f45a142fc8e66da61734830136a50da8ca05f01a07de9e3e315be87e29
COPYING.ja	644	2.06 KB	ff6bcad6dd598e328541552b374cda4dc8390c1862da051495fb3afacd562c88
lib/bio/appl/blast/ncbioptions.rb	644	5.46 KB	c235d8a19b5ae1fab27bd916a0527055561c99ff8561e6cc0a45cb475fc3e30f
lib/bio/appl/blast/remote.rb	644	2.97 KB	f7daa9196e338119cd7da7d1b24b92e8646399a09f4a44e2940f376ff991564a
lib/bio/appl/hmmer/report.rb	644	14.2 KB	9c3e92e9f168c849c3a25c7605fd6f834884c2f60d0eaf5530a9fa5cf9a87e83
lib/bio/appl/meme/mast.rb	644	4.21 KB	e0e0743cc84def20196759b628e5c1c2cd066bc4260620978ad0cd532ae61a9e
lib/bio/data/codontable.rb	644	23.1 KB	c8d70c49adae499da24d27713cf541b4a6668f5c63c0d531edb0a2b82ccda129
lib/bio/db/embl/embl_to_biosequence.rb	644	1.7 KB	68591ecd39e1f856e9c55abd8b471514f64db35b8e14ef39eb3a1470c1e91096
lib/bio/io/dbget.rb	644	5.19 KB	e9f4133b481f5e2e4ed1f528522f145b9249d6fafc5b40a7c8e43e813cb5cc8c
lib/bio/io/flatfile.rb	644	13.3 KB	84792c667f395994d596ffed28458790133c913524acbe3f9e65d70cbd023d5b
lib/bio/io/hinv.rb	644	11.5 KB	b9026fbbb91e2001566a67a7de559da99d19d1fdffdcee161019332abced8f77
lib/bio/shell/plugin/flatfile.rb	644	2.29 KB	8c296ec5abb50e2071a047b4a4cb34f32dd436dd17dffd6915e34ab0e88fd3c7
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml	644	103 Bytes	69cbd28d0be4a6e87e3360dc027f45ca0d98e1bd651cca345351928f13e11191
lib/bio/util/color_scheme/nucleotide.rb	644	690 Bytes	826ecc72308f879c325103e36a5dbe51fe67ec5b9fcf32e73c133ceeaf80376e
lib/bio/util/color_scheme/turn.rb	644	1.24 KB	bd3eccff3a257ba853884956d26e8da73b68412375bf9531af7964a991ced74e
lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb	644	4.08 KB	6800d44c6e6a18e877d1b26b627eb305aee5dbba25cbf6c6909a09c4a2c91b99
test/data/fastq/README.txt	644	4.83 KB	aca3f26a1c8d8bab7dca1e1cf8ba73d14d3ae34575f8d348b2ab5eb4d365d5d8
test/data/fastq/error_trunc_in_seq.fastq	644	535 Bytes	6e7bf90bde5e7b011d52b7b4c956734818b9a52fa04a34e978d3b405293b7fa0
test/data/fastq/sanger_full_range_as_solexa.fastq	644	550 Bytes	a7ce416a53df877a08592025830be338b345330c61064ce2499532f6a2497d40
test/unit/bio/appl/paml/codeml/test_report.rb	644	1.29 KB	1232231ebcda2f8754188a0a491a110ef91bd69901bd92803195adb6ac6b93a1
test/unit/bio/appl/paml/test_codeml.rb	644	5.31 KB	5e6bc2dd067a706f06ecab978dc95326f651fc46bd4ed3d4e84bcd1acdbf2793
test/unit/bio/db/kegg/test_glycan.rb	644	7.91 KB	bc115109fe7235e055cc5fa154289195c617baf8888c818813ffb2d7d6ef6dc0
lib/bio/appl/mafft.rb	644	7.14 KB	03c8da2d5aef2ff37488e33f03a31697a9e91590840ce2221cd3cf83bc5e65dc
lib/bio/db/sanger_chromatogram/abif.rb	644	5.16 KB	35137a2bf5e99400ce8f9f7ed58cb70ebb2263dda5db2f91d7df9c1bdfa24c09
lib/bio.rb	644	9.4 KB	47f24e1166e987ac60decbc2c79a4685664ca9114d1b987d7b56f9f49b3c70c6
lib/bio/appl/blat/report.rb	644	17.7 KB	1c97d4b9deb9901ec00ac643fd795812aa9bf3c687fa3f89bab91b7730bb3376
lib/bio/appl/psort/report.rb	644	12.4 KB	a6d4f66696a5cc9a34df56e9c6921098ae27f2c0e38284e58ceb1b558cdac8d9
lib/bio/data/na.rb	644	3.62 KB	3371130fdb20389c12ffd8d3778c8860993c89f1992884552146fcf8bc3d9b9f
lib/bio/db.rb	644	8.14 KB	63ef9fcaf06e37eb4e88d3040881f7689d6f99b9e75cf8f2824f8b82ff9e38d4
lib/bio/db/embl/format_embl.rb	644	5.76 KB	6d5899a54364eac80e657aad9bc4d4d7bb64c2695e2ea028a1030226ed1c58fb
lib/bio/db/pdb/chemicalcomponent.rb	644	6.67 KB	498ea530e871471899667b03b944151b291d662c51b0732a44ace5386f492211
lib/bio/io/flatfile/buffer.rb	644	5.84 KB	3f9dc74600896dafff3dbb9b4594a5dc23592d4f89b27d548cf475e272dea56b
lib/bio/util/color_scheme/strand.rb	644	1.25 KB	875060462cd79b26800c6a6122c21083fc55747ed85325162db2ac21038a18b1
test/data/fastq/error_trunc_at_qual.fastq	644	582 Bytes	894945d96905c98e3e70d10b25e7ed702f151da44d4f4d56e7a479f30e844bd0
test/data/prosite/prosite.dat	644	167 KB	cffe5a81263ac7e3877bab8f7d32e27ea722411b4d4f0fca235fe4e552fae671
test/functional/bio/io/test_ensembl.rb	644	6.77 KB	28e516bde78e0a3673b5b9ef645ce241cdd0f2738a88a28285e5d495b32c600d
test/unit/bio/appl/meme/test_motif.rb	644	1021 Bytes	bb29d17b6cbf8a5918072b542763d87cd8223f86d7c6f14f27b220c97b5fb4ee
test/unit/bio/db/test_fastq.rb	644	27.8 KB	3e4131a05297b5dc7082af3e1efffc294a7ea8f51768df0b758fd4498fd08ee7
test/unit/bio/db/test_phyloxml.rb	644	22.8 KB	0250e09482407ad9c1bf8e2546cd7f186f59e881ee6b67e368224c1f6193284d
test/unit/bio/sequence/test_common.rb	644	10.3 KB	e277eb85dfaac0c2de9d878019b41363df80194ba76f9c568e874aa31e77b025
README_DEV.rdoc	644	9 KB	f301218691598b235e5b0a8603bde7b5bb302376f2b0eba14e101e666b152d13
bin/br_pmfetch.rb	755	9.87 KB	0d44e2b56f2c4c0b759acbecac01e557343eace38a2d05f616d6d72aa17a9fba
sample/fasta2tab.rb	755	2.33 KB	ec5e4a2ee4cc4f219cb2274886beecb8485edc60b6d8c04e8c3a4f4324455028
test/data/KEGG/R00006.reaction	644	730 Bytes	74cfc3e7fb48400b5dcbbafd58647809acb42fba4aaf5fb53dc83c901269b9bf
test/data/fastq/longreads_original_sanger.fastq	644	9.24 KB	09b5f250b24d2744fdcfb49d5372ed92666e4d6d3e694a466509e2f179880261
test/functional/bio/sequence/test_output_embl.rb	644	5.32 KB	cc9df3add69492bc7de5a48d2bb12cc8ebf208c09d238e3204ef29e6af88c476
test/unit/bio/appl/gcg/test_msf.rb	644	4.45 KB	88a50ea29fc6c3eccea1c97eb35ef75bf79e68d2646b15b99fb1f3e0df50972a
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb	644	2.16 KB	57aec6958b4f00e82ee882aed1a49a1725bb14d96d33667a212ed90aeba6a4cc
lib/bio/appl/fasta.rb	644	5.84 KB	1c08a4018fc4e34f195ee25c0dfd0d25172bb9565579e68752ec51412da6699e
lib/bio/appl/phylip/distance_matrix.rb	644	2.63 KB	24455644af9afe549c082972df362c5caa3d3eea3db29b2298f975a05d3c6626
lib/bio/io/ddbjxml.rb	644	10.5 KB	e2f68dbe43b6d87aa27ce01486054fd702db45beaf6a470b4168d3c9981963fd
lib/bio/util/restriction_enzyme/range/cut_ranges.rb	644	1.21 KB	6367e63e557c219111df6e6d2006e7545db7d40082e7874a6bae643f870fc174
lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb	644	2.5 KB	7a189f653796e06b5666065f52815594373ee505b600a8414aad9db17755ef97
sample/demo_ncbi_rest.rb	644	3.48 KB	ede3b871491e386f854e9bddce1f08e7c05e04f36efb5bce28bfaff080d36329
test/unit/bio/sequence/test_aa.rb	644	2.53 KB	15d484c50fa839ee6108254bc0e8a6551964a55a2f4ea5adcfc4d5343eebc92d
lib/bio/db/fastq/format_fastq.rb	644	5.37 KB	353d58684154823306f46966bcda7f2269ea804455ec0ba998aacd6d25cd047f
sample/demo_kegg_reaction.rb	644	1.47 KB	3b5f4b0c869458395fe10b94ad20139efe265c5d4312cf4f7e7f7dfcb7904987
etc/bioinformatics/seqdatabase.ini	644	3.41 KB	0a930f4502c1dc0ca6adf2ec50c2bda9e8b213d618edb2532017e9443ab58d9a
lib/bio/appl/iprscan/report.rb	644	11.7 KB	a78cda0bb4a26de10aa6408262f8eacdec6a27dcbc0d51d6a81fc7b3c3154d80
lib/bio/sequence/na.rb	644	14 KB	6dd67df64f7c5d893060d9e8aeceaeba1b8388daf9ab3edb1d1671172f9fde55
lib/bio/shell/plugin/codon.rb	644	5.95 KB	ca5ea167f8b0dffd44bbe810c3ca77b22e8eda146da319a12267d5d4b06e192c
test/unit/bio/appl/bl2seq/test_report.rb	644	3.52 KB	1f478235c31f939714066745348a7a032110be2e9483822e85e40ae0c8993358
test/unit/bio/db/kegg/test_reaction.rb	644	2.99 KB	c7084af4afbb8495119c99989df5e0d1504ce64a908448dc8b5b15cbde1c8a56
test/unit/bio/db/test_soft.rb	644	6.58 KB	07217742bba9f0c0fa11324c06d074c50b06ee491fe5b37bc31656d089065e05
lib/bio/io/fetch.rb	644	6.52 KB	1c940010dc593ae8d4e899dea631476724463498db97194f4b720ec67ae9acf0
lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb	644	1.76 KB	75460543e7cbc0f4892791acef7855df597d6904fceccdd999074725ba0fdf78
sample/demo_aaindex.rb	644	1.33 KB	9a4732eefb18e0b31d258319c33a103f8e2e0a976e812a1f8f834efd417e155b
test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb	644	2.39 KB	3fab574dbc9bda283038255d49f111c16d0ac08ba3abc9bc71bfd6f7775ef3aa
lib/bio/appl/bl2seq/report.rb	644	4.4 KB	6e2e7bd629b56949f9f38e53ec9fc4749f04e4f19a02bebfaa5954269b0f4802
lib/bio/io/das.rb	644	11.7 KB	3dc4325f8d1cb9484c1446a20faa7c989525c7afee79070fb9658681912820a9
lib/bio/io/ensembl.rb	644	5.69 KB	44668eb1edef70d1df9aaac87d582b155986f00507261b236984132e8383846d
lib/bio/io/ncbirest.rb	644	22.6 KB	9cf7eb86f1bd2133bb15e723da45193ec6d26b260f922d20bbe92d0d19973fc8
test/unit/bio/test_db.rb	644	1.77 KB	4f991f62f786ac3b05a949228e5538038163a3e6bd85041c74934d084dc7467f
sample/vs-genes.rb	755	5.82 KB	88f460be7dd0ea6961a364efb8ffa2037dd20636234803968dbd99db783cfaa9
sample/demo_das.rb	644	2.23 KB	f193aaa863e90aba9bff5f2be0ae191a552f6693b81df4b13451149ff751dc9a
sample/demo_fastaformat.rb	644	2.43 KB	e5522eca1e7c5fdb2c853df473ef6f1c607bd65ee646cd8bcd8648af5f03dcd3
sample/demo_kegg_drug.rb	644	1.27 KB	6852a6cccce5590fae8c7963961eccde179204ad461dc350be5256f147612264
lib/bio/appl/paml/codeml/rates.rb	644	1.9 KB	12567fe7006ba7132a429618989bf69bfe47e2ffbdc9b5d86c06b0bcb91bda5d
lib/bio/appl/sim4/report.rb	644	17.3 KB	9482280372a299c66ed8a073cbf433db28caf5a9fa7d5257f7e2312aadd38ce6
lib/bio/db/fasta/format_fasta.rb	644	2.91 KB	6159abb9e804c087998e215df6cd4ff96d1e72a8bf37ae20a92f6a232645e632
sample/demo_locations.rb	644	2.9 KB	6d199174abe902c5fab571b53d33c856aa2e4047b823e76af4bbac253e9a07b0
sample/demo_nucleicacid.rb	644	954 Bytes	5d0374ea992c87e9c08d3dc63629ec5a2aa3f6fa2610cdd08f5b288f18418591
sample/demo_sosui_report.rb	644	1.87 KB	450026b68483c8a78bce3df8be796b49e371c137e4078c9a39322dd7698dd600
test/data/bl2seq/cd8a_cd8b_blastp.bl2seq	644	1.54 KB	bacf6a696044c0751edd37d72025326ac19417e39f76139e1ac568d54c098e2f
test/data/fastq/solexa_full_range_as_illumina.fastq	644	450 Bytes	cea9449b8602d7a29b6eaa45a0ecb2edd3e25cb3273f1476e05ffd3766da7cbb
test/unit/bio/appl/test_fasta.rb	644	3.16 KB	f121d02629730c5fcd79783a6209b04dc2f0a4a179b07aa53a71c2eecfa74e34
test/unit/bio/db/test_lasergene.rb	644	8.38 KB	67b1662f1f1003cf9dcd22755c51297002ecedecb1aecc1fdcb1c49da0014bf3
test/data/KEGG/C00025.compound	644	5.2 KB	837ef41867587872d0b0a53f66f7b50093249569516e0f815721b722b0f32871
lib/bio/appl/blast/format0.rb	644	44 KB	bea29bc4c5157f946bc55f2ff99885ad2da3fe5a8b00bad51261193bb366773d
lib/bio/db/phyloxml/phyloxml.xsd	644	31.3 KB	87a501154f63e987cf93e11af44820e2fa80b0ff56342c40a25d8e2122ace0d2
lib/bio/feature.rb	644	3.93 KB	09be26d2058b8f85fb1f0a9034c9aeb779ba667338d4da831520f0f7ba0e31f3
lib/bio/tree.rb	644	25.9 KB	0c83d24006c09a845743a895a807fabd360420f32e343c65bc8ed96cb4fd8560
sample/demo_codontable.rb	644	2.84 KB	0c63856ae537ef03835eac5827efacfc9f3f26c85928f2e89cbbe8189dad048a
test/data/command/echoarg2.bat	644	8 Bytes	e4647efd47d7ad4edca4f3725a4f9610157cbc8fd9023666c3183400120b2358
test/data/fastq/sanger_full_range_as_sanger.fastq	644	550 Bytes	daa8500ee0d0b8242c65991f4965b1ec445cf9f57565b838d3ba760e5313cb00
test/unit/bio/test_location.rb	644	22.2 KB	280c4dd0fe07544fb6e6dccac33405d96d6c9b294be914bf345f6835a11a08da
test/unit/bio/sequence/test_na.rb	644	8.01 KB	dbc562dc4a5a8daa94fdf5616a9f06a1625909f56dd0521fff9f6cbd0ba4cff7
lib/bio/db/fantom.rb	644	15.1 KB	df4cb4028ff7f360313e1ba638968c6c55ac99890a10bf76fc759a0076ee46ee
lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb	644	949 Bytes	d9f9349d45f95f3e753b7b8650da42e032ac0bc3db6a8c5db0d4ec9b4c7a8573
lib/bio/appl/blast/ddbj.rb	644	3.8 KB	9afff11a382502f7ce96271e2a97da8bce7bd26436d35480682064e91f9510ee
lib/bio/io/biosql/config/database.yml	644	379 Bytes	d395d83802b9d76d291add20f85d110a8a63918dc3b62dc13849b311dbf110a4
sample/demo_sequence.rb	644	4.24 KB	61b81c325020c522e771fa6229a45c0ea3e82ab1bdc9e019e45848e7a548819f
lib/bio/util/color_scheme/buried.rb	644	1.24 KB	9904524d8f999ef83de1568d72809c1999cece53397c655ef8776a78a38eafa9
lib/bio/db/medline.rb	644	7.3 KB	7f3f23fe3ef044baf9612bdb92d70e5248d7f49e694e65851492fa3781451717
test/data/fastq/wrapping_as_illumina.fastq	644	963 Bytes	cceaae4b9273ceabe155ab40724f96d56c725b920fa94ddeb0a0c21f9fc8e0ae
test/unit/bio/db/sanger_chromatogram/test_scf.rb	644	4.39 KB	6d53c01e8e22a260a13d3d04f16ffcc237bf156fcb08acc485837725df115418
doc/ChangeLog-before-1.3.1	644	127 KB	9f6d16df3336cbca579e1fd90d0bba50878442fb5403a9ea3a7f0d13f1c51823
doc/Tutorial.rd.ja	644	84.5 KB	756b9f88e407b386c64292e1f4411e0ca21ba1eba837b284972bb929fccceb62
sample/demo_tmhmm_report.rb	644	1.36 KB	a6517a2b8fac40759b81953333a3309cf1b89aaae0fe31a194c021947ed965bf
test/data/gcg/pileup-aa.msf	644	3.4 KB	94a8f78752867af033bc76e9541f8a8a1e5ad2c52030364c6655bb3a8f1b7cb8
test/data/iprscan/merged.raw	644	7.47 KB	5eeed06ce72f5e9a2b6c1b8cd95daf17c8df82b1e926056dfc089a141a1177f1
lib/bio/io/higet.rb	644	1.3 KB	8d6daf64f8d2f1395102a877163cb75af7f1a35f2415ca702047e83c3bdc14aa
test/unit/bio/shell/plugin/test_seq.rb	644	4.39 KB	16e6f21785caede7a25ae34504e75bf559cd90dd26c369372585ef7569df5917
test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb	644	10.2 KB	b81fe69319e35852270f6bf71d7a15478c7db84bc7d77d210f8b49bfe8dbb92d
lib/bio/util/restriction_enzyme/analysis_basic.rb	644	8.21 KB	2abfa2c7a42e0ca3c6f0aa857f044aaed1f22b6013159c7bb20c9d04ca7ac04e
test/data/rpsblast/misc.rpsblast	644	7.26 KB	9e44883a6a78e25db6da697431f3d64a6844cc4fd05d39e2bc2eca7b4cf428c4
test/data/sim4/complement-A4.sim4	644	1.28 KB	49975dc65d349b605448e7248be76ae2f91fcab52bc9ae14e45d202bfa21f244
lib/bio/db/kegg/kgml.rb	644	5.86 KB	e434a73f1002214e20d3be9691f0620156b0cde3908bfa0bdea0601521fe53f4
lib/bio/shell/object.rb	644	1.11 KB	9a46bd1a61c6ac95c55401ac345aa31a7fc5ca2243cb2c8a7414c0d1b2ad3b78
lib/bio/appl/blast/genomenet.rb	644	8.12 KB	c69cd85d2b867fb389f72e80549dc3f9eb619b26eafba0e130733157f0e83769
lib/bio/appl/fasta/format10.rb	644	8.83 KB	b9763c282791227f42f8be5e81bb97bcca921c417843fd924d3aae6918ff81e9
lib/bio/appl/gcg/seq.rb	644	5.41 KB	4aae0d8bde943bf48bd28128c9a9206ba0d75a437420f3023c58d0035edc7f40
lib/bio/appl/genscan/report.rb	644	8.4 KB	1d12602273dfe6e191ea38af1e4ddf5b9d87a80e53f3768b4469e2dcec801e0f
lib/bio/appl/clustalw/report.rb	644	4.46 KB	5200a055639043299fde52fa1c7dfcea0aea0f035270a157709f2f8799850b96
lib/bio/db/go.rb	644	9.84 KB	6a3bdfc00cf935cf10009e9fb5032c30ba051c94fe5c8a093396b3e8f041f0e0
lib/bio/db/gff.rb	644	59.3 KB	6c6584dabb392a3cc562c93445a2dc8a898a97d2ce759ec5210631a8d4a19133
KNOWN_ISSUES.rdoc	644	4.07 KB	7e8f9b29f53767127f4821fb74d0f4d4f8159b3a6dae8c1263deb23babc905bf
lib/bio/alignment.rb	644	73.5 KB	d85b3b451b67e3e8f3068da46d38bb608b6c4f67cf9c9e6963e88cb828e3cbda
lib/bio/appl/blast.rb	644	15.1 KB	f51bc601534771d4899a95d9d30aab59aeef5953aa4e4b01a196af5c2e118fa8
lib/bio/appl/blast/wublast.rb	644	14.2 KB	2413b48ffd1d271a49f5ae57c323223fa79b008972a5b59e911f59c1cd01ea33
lib/bio/appl/emboss.rb	644	6.08 KB	deb9645f09998c1f6f5dbef7a97a2e5fb491328634ab4d50f09b2f1afa8ec2e1
lib/bio/appl/gcg/msf.rb	644	5.11 KB	c7c41a817f780d45c126c42e4fa1e78ebb986e9e0596f103f4627001ec73585f
lib/bio/appl/muscle.rb	644	1.37 KB	3913777ac7be3249cd810bc9718b5cad5c33f1baf8b81f86176551db71436bc5
lib/bio/appl/paml/common.rb	644	11.1 KB	6ab2be5c82923922eb79afe7ba71c40e5be8032b732ec9b5d282b9599a123372
lib/bio/appl/sim4.rb	644	3.3 KB	0738d0d14c2f1ec99a5125831ae2ee3c3de5f09ce6489ee50e9eb82e7d5f2662
lib/bio/appl/spidey/report.rb	644	19 KB	e7ec75fc26c812cc81deaa8653dfba4418ce4910a4ae63cc6dc6e938673b17df
lib/bio/appl/targetp/report.rb	644	3.86 KB	ea6395dcc172bed3f4fefa7d6632b622c9494d6c5b4d747002f0f23a25b52f3a
lib/bio/db/embl/trembl.rb	644	1010 Bytes	75b1c109bfff4503e62e67c940d16231d736ec49e604dcffa43c009444f19477
lib/bio/db/fasta.rb	644	7.17 KB	a71804800c414d75da4e3c0c2c398fa90a04ec6dd0356afe7bd386809549e7d1
lib/bio/db/fasta/defline.rb	644	16.2 KB	2b181c20f6ca49acec286fc92388ad607139e4f65e92158760e3cc3163075a2c
lib/bio/db/fasta/fasta_to_biosequence.rb	644	1.51 KB	be1fbf4bc481f11772ca1961afb6187ee7a40073254fefad0010a42d88a6d731
lib/bio/db/fasta/format_qual.rb	644	6.16 KB	bb807fe7cda248aa7bde8d7adf16c3b6d2421d822af2c01f6ee0529a4bd944f6
lib/bio/db/genbank/genbank_to_biosequence.rb	644	1.75 KB	f09815c7600e410e67356fddcf4ccc7f7c1894b1903a942a5c86cebaf1d36413
lib/bio/db/genbank/refseq.rb	644	380 Bytes	71a2c7417d6a1aa575717a4bbd08cabba230008cdfcd326e5581f44bda7cb358
ChangeLog	644	96 KB	f61fa09d1d6d8f8579c9ba570df71e7b959787278e736560cb0d21fb0e5b942d
README.rdoc	644	7.85 KB	8a7553c990bf7b43e907cecd64f6177cf21a8f7d1b08c16cc80e034d4c9d6366
bioruby.gemspec.erb	644	4.02 KB	8d71479e3eb9d6b7dc31d7f53c793358f82679d067035e28e109923871c49381
doc/Tutorial.rd	644	47 KB	7fc771f36f43360480c4795a38891c8a9c7b7a6ebe4f1a33529cb7c4fa80f1f1
doc/bioruby.css	644	3.89 KB	98fdbbc2192ddabce70ca48125b00fc1bced6fadb2ea46d42e7889638a7e6799
lib/bio/appl/blast/format8.rb	644	1.94 KB	e5de459c710c3a819f17ed3f6e37ff708dd34b040ab063191418911d01581e0b
lib/bio/appl/blast/report.rb	644	17.1 KB	c7bcbfaa3d4be250c54f31cdc77d8fee7e97500d34266bffa750e554c917f507
lib/bio/appl/clustalw.rb	644	5.98 KB	1e51eff966b274cec63a5d10e2ac61cb598b9125163c63ac4b9a443b23c1d1d5
lib/bio/appl/meme/motif.rb	644	1.04 KB	7176b41894d500bb58fb39b86ba1e71601b5d8edb4f0054347c6a529ae6e8e19
lib/bio/appl/paml/baseml.rb	644	2.74 KB	57e1ba4b3a8b914c9165e6ac4c99e9c8d3229bc6bab99c4befc99e0fbe4c8808
lib/bio/appl/paml/codeml.rb	644	8.08 KB	2963e78e496f52758c67a34e65b8377dbea10ab31141a7560cc9fa782a23d6c2
lib/bio/appl/paml/codeml/report.rb	644	1.75 KB	6c71c6032bbdbb748ed3a5523fd4236888347e2c043b633ff71b66bf9390e483
lib/bio/appl/paml/yn00.rb	644	2.79 KB	17fc612d7db16c1035adc7979da1d611a667210fb0a6bc94f50e7b6b600649cb
lib/bio/appl/psort.rb	644	12.1 KB	57e9e08d484f82b9b0481fb4a045b6279b3145655d6f58b71695e191d9e913cf
lib/bio/compat/references.rb	644	3.59 KB	2c9b0a6ae3aac34d26693af51bdfaf847df0d4813d6d8984f9c11de8151fe744
lib/bio/data/aa.rb	644	4.89 KB	378b8e509427b76a1936c0a8ac05803ef6d42a3ed94b7897ae4b0c44a3fbfbea
lib/bio/db/biosql/sequence.rb	644	17.4 KB	f331f5511cd1fa32e5c14fd1c12d0a46cc8b1a2a26fb6301e417ee685383255e
lib/bio/db/embl/common.rb	644	9.55 KB	64897ad1d95a525b5d6cc5a07f8ec848c1ae789318ff91b1e0a2ad9f9d8f9a9a
lib/bio/db/embl/uniprot.rb	644	951 Bytes	af4e716ecf160c6d3b1e48b8bdba8e449f388d0babc972a77f76d5294bea7d9a
lib/bio/db/fastq.rb	644	16.9 KB	981126a81250c0197b40b9f818cbecd6523aded00b0f030d94b30606fa9a9ed2
lib/bio/db/fastq/fastq_to_biosequence.rb	644	900 Bytes	d54dd813f68f84101914ab4790e19d16df526a577d33f2f34e273d8c5ddf9696
lib/bio/db/genbank/genpept.rb	644	1.22 KB	8317e99c04999c216d5234034ecbfad0c679ca42d5e8793aab551fc8cfba2f7b
lib/bio/db/kegg/brite.rb	644	639 Bytes	88a3057e5f31e1faead4b282b0a6ff1a1806f388cde96869602eccd834ce6e9b
lib/bio/db/kegg/compound.rb	644	2.51 KB	202f1eeaa6715d177c7089c13d30d12eb8edab28a3a8e21f05d66652b07f7e95
lib/bio/db/kegg/enzyme.rb	644	2.88 KB	4ddd7fb884c937f033ccfa53c3534c99587589cec3b1189fe61ce65a6c93e6e2
lib/bio/db/kegg/keggtab.rb	644	8.86 KB	8746e7d99d099528bb6c32cd2b15f075d7b51a6c6f1afc515e72a29886d7555e
lib/bio/db/kegg/orthology.rb	644	2.01 KB	68ba0a6b4ad3c0e01ef6cd4f22aa99ff09cc8077dc9acdc16d25dee6850fd32c
lib/bio/db/kegg/reaction.rb	644	3.13 KB	1295d6448e86fbba22859710d342aa9d92bf3a46f8999523c9d7123b55ebde26
lib/bio/db/kegg/taxonomy.rb	644	8.5 KB	ad8789074dfa2c0331e0f3aa876c4acb61fc5558ca133ec83cc2782dbc85677f
lib/bio/db/nbrf.rb	644	5.2 KB	662f0b5ac3817bdaee7822faa93d325fc268dddfebcc821a2c240fc1a68b9f17
lib/bio/db/newick.rb	644	19.1 KB	7396214491bf02891e0a4b3b29700a7a69de03c8f61c5424a75f6fd0cc8f079c
lib/bio/db/pdb/model.rb	644	3.58 KB	a138edb845da576744c234294fa74f9ca0d41e800beec975a2d7f4367b619595
lib/bio/db/pdb/pdb.rb	644	62.6 KB	e757f1ebea0ecad925d75986878218685a97b2da0f360b19ef55c3cef1a743ed
lib/bio/db/phyloxml/phyloxml_elements.rb	644	35.4 KB	4a1db8bfae008195b929096c7d97a4fe82b17cee4e6aca305aad9e69c5131b02
lib/bio/db/phyloxml/phyloxml_parser.rb	644	28.3 KB	9720ad9b91d8bc13789698de86e89b54ca5df3c5a00962f11b1903a86a285092
lib/bio/db/prosite.rb	644	11 KB	827588b748f43c7dabc13662d2f97cc3460bf41963bb86912bcf56e55c1dd6d9
lib/bio/db/sanger_chromatogram/chromatogram.rb	644	5.47 KB	4b75daac4400123c02db03fd72bb790ce0ff9a9248a884f31ebd3e35650edb49
lib/bio/db/soft.rb	644	13.9 KB	8ae1709b5dbffcc8640e617f142cee69c5fc9c5db00914c0743b2bcd0fc5bdd4
lib/bio/io/biosql/ar-biosql.rb	644	12.4 KB	b1702ec502c7c4440bf754e052e87028dd7879726f8b3f997146493933590627
lib/bio/io/flatfile/index.rb	644	33.5 KB	d73e284969629cadd7d745abae567d92ffe60df0e76c2dccf1aa498314546b23
lib/bio/io/flatfile/indexer.rb	644	26.8 KB	07b629888b34645ac50a2b011dcb61506c655648b79580040cead344291bce5b
lib/bio/io/flatfile/splitter.rb	644	8.24 KB	16cdfff3260ceea21e3993cb0983e4b9dfeeca0aa75cae5a4b91684b41f6baba
lib/bio/io/ncbisoap.rb	644	3.85 KB	1401737fef61449581e04886f1a2a7cf3e4c445c89052249da22f58870b8ea54
lib/bio/io/pubmed.rb	644	6.15 KB	1e1eef4067b407d767c6f12d171ee50af819e7184f46aee04f2a0a6e5cb5f92b
lib/bio/io/sql.rb	644	2.61 KB	654ee925ca98024162982c5a6aa4b258761b8667179dd4990abd26d9c6e9c4ae
lib/bio/io/togows.rb	644	13.6 KB	2ee9c00bcc31da5bb257ac40bcb763443376b97873da368abf3321aed2a8aa42
lib/bio/map.rb	644	12.8 KB	97165720a85cc9a617919ee4d87f5b05030a2805856c041314a8982325c4c71f
lib/bio/reference.rb	644	18 KB	8d01e9da2188572707391d96e9f3fa3c622ea4071ac5092b4ed0c1aca318856f
lib/bio/sequence.rb	644	15.7 KB	ef38d7c7854b5cf799bed5abd0473955517d0c72fe3294158cb4be366fbc7431
lib/bio/sequence/aa.rb	644	3.07 KB	a9367cf1041fdea91b141dba7f998096146b8f12921ae2d7c188d42736804f3b
lib/bio/sequence/adapter.rb	644	3.59 KB	5f196f75845a08e6d5802377b995d35c5a4167e0b30e6e1c1085929c1f539cde
lib/bio/sequence/common.rb	644	8.97 KB	85797f153415b943963e80ace9e14997abb17047b65d0f7a24796d41ef65951b
lib/bio/sequence/compat.rb	644	3.66 KB	a7f4832f075eee502b4ed59d4facc5a7f4c52082719123797344c6e15a81a36f
lib/bio/sequence/format_raw.rb	644	530 Bytes	aa149aa8d9b75a2d0e4acdc3b6e2ca19e5357050c5a02587f9fe59ec584c2161
lib/bio/sequence/generic.rb	644	428 Bytes	40ebce47a9323f96fa8e8428aa20cbcbebdd34b52ebbe9547cacb22c98f33b30
lib/bio/shell.rb	644	1.01 KB	68266bc83b722d191ee2c9b8798da0981367dcb6b13769a55d348389aa0169c6
lib/bio/shell/interface.rb	644	4.34 KB	be478421babc80cccf2b9d506c6c0c4fcd28054cfb07c8833b0d716d9b3c6377
lib/bio/shell/plugin/emboss.rb	644	378 Bytes	3c672cb04ab61b3a2fb7f451a8a4e7e87be843b2353095e0c7fe3d6257c68bed
lib/bio/shell/plugin/entry.rb	644	3.57 KB	e3199c0c134fe846e1d3502d7ef4abb2c9a98a5d21c595e39e608ccbd8e46750
lib/bio/shell/plugin/ncbirest.rb	644	1.43 KB	01d2a0b7e8ff3940b879e75792a287d98d403b76ee560af8347ecb037c4bb192
lib/bio/shell/plugin/obda.rb	644	870 Bytes	b5999d927691ff7a320fb474e3d2376e0d302feefb657efa9bc3e2d544967407
lib/bio/shell/plugin/togows.rb	644	1.09 KB	20b6827c803c3173a31db7edb94246f0ab6bf715c7f0501343a6d75e09f1b4f6
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb	644	1.44 KB	bf6c4843686cf1319cf6c94b146216c65279c5b479f06b66784178fbf180071c
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml	644	818 Bytes	b494b8150835b9f21b8e61ef20b6a063a8f485af7e4176d9941369224a9670f2
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml	644	215 Bytes	f729f88b0e7b5f80f1460f30cd59cb6d4c48c9f0b19ef147c7d706019f4a6939
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml	644	110 Bytes	d673ed625540297e132f32b8c8f5298f7c6876386d8dc307ba9c44bcb8075bb5
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif	644	2.69 KB	0a62ede00f058222991d080db3b08ee22298ea956f4b666aa14c82fd747ab695
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css	644	4.8 KB	bff86b2ccc5c0fa51a0f18ea1c078f0cdb1e1d46c82814a60905d319f06bd103
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml	644	1.2 KB	9bc0d74504629bf7a5a94a83855c1f650463073f01ec0ca592bf6b771beea1b8
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb	644	3.52 KB	5cefaba3f464ae203e4ddd96bf705384f9790f5658a557ffc4faed55ebd7bc92
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml	644	219 Bytes	5dce1def10e5e98cbe02b490c0d1facb3fa0295b38fbbb4d272b1587592bfdae
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml	644	918 Bytes	b6b12f77b3c97eabab267cbb5f1bb3f38d6441ac09bb3f91a15383722971c7ac
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif	644	1.51 KB	e008bc0bca2fa6f9b9c113fad73551230961baec88c06b20997ec50171bb2b6b
lib/bio/shell/script.rb	644	476 Bytes	5be184d23bb6de666291ff4bfefdd1293d1dbc5cacd63b00ac8c3124e3322c90
lib/bio/shell/setup.rb	644	2.5 KB	8fe1225a57c89d14f61594b0cd2f6411bb3a33f90ce805780e19be7e3e349a25
lib/bio/util/color_scheme/helix.rb	644	1.25 KB	565b1a9f94431205873436ba4a2ab2a3e3267c9bf3e0cce246ef661c49109ef7
lib/bio/util/color_scheme/hydropathy.rb	644	1.34 KB	8b827c40b823eb57874ecf65156a8ad9ef2ed1278be7050e3e8e7ba5f93061e3
lib/bio/util/color_scheme/taylor.rb	644	1.07 KB	1af407d819e588fd266b4076e08849c3f7fe6211cd9799b8db2126286ee5e17e
lib/bio/util/contingency_table.rb	644	11.5 KB	7bab709b1c62ab19a16546aa53907d700938d640957e73a9a51d40fdb3c997f1
lib/bio/util/restriction_enzyme/cut_symbol.rb	644	2.65 KB	486d4e9af1af0417779b3514701d7a748692b007a9645303f86e2ba02e919186
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb	644	1.02 KB	bef996cd083852621ca8ad4835467e0cec36c896641dddff73ef6601cbf6bfb6
lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb	644	3.17 KB	b52e94099dfdd4d82dc5cd5e05d0d25d6e70f2d1beab41ee6b38169c837b45b3
lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb	644	7.89 KB	119c0d89e79b45de078058c0a33c320f69cf89875f088f6d9f789f6e211ab8b5
lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb	644	1.27 KB	9787b52acc8e9dc5ed6a283e85c719ef895b95fbc03d74726d2a6b4d414965a4
lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb	644	3.97 KB	6179c8fdd0d215eecd48e63a89121de5da1e228bdf7158d5d5c94f1222a91ab6
lib/bio/version.rb	644	700 Bytes	ceeeec324580c089eb2595d75e4a297acc46bd41f30c00c64edcb16c000b602a
rdoc.zsh	644	265 Bytes	9ee45c275fbb315074d2981bf02dbc9a6199636644129056153d262ff7399b7c
sample/biofetch.rb	755	12.2 KB	0e2e2a35cc2970bf0cefaa6d4befb431082a0391228435cb9f15df3ded3970c9
sample/dbget	755	1.17 KB	04ccde1383182e2490158b2c6b5fde219e2c9b15c46b4572a79e6d1844d6a7ea
sample/demo_aminoacid.rb	644	2.92 KB	5d66a56b5c310f5bddd0e2440baa20cf5a2ca1013c25d5b90b05c3f85130b7f1
sample/demo_bl2seq_report.rb	644	7.57 KB	0ea9c4221095bb333fc585aa330d12ab60677c96b849aecaf72f2a4edda8e921
sample/demo_blast_report.rb	644	10.1 KB	af533f7e723ee515ebfd88e973bd52efb89dc883b365a9606656c9c9ceb3f162
sample/demo_genbank.rb	644	2.48 KB	7093bd7cd51c642086901daafac00db41bc63c44947a5fe7ed4aeb72cde63e4f
sample/demo_go.rb	644	1.96 KB	dcea1de08e22bc7963396a1dd74e7cec68feabc3a4a995968921d70cbab33a93
sample/demo_kegg_orthology.rb	644	1.3 KB	c6016b1bad4fed0612152aee694b32755412fec276a9cb157e2626519f97f4f1
sample/demo_kegg_taxonomy.rb	644	1.95 KB	6f629b78ca736be1b0cac94130c5d069c50202b46f8139f411647f0042469084
sample/demo_keggapi.rb	644	14.5 KB	b12fd6ba43895bbbec3004680cc2f01d5356b24ec432c0398b6322aa4c12ae69
sample/demo_pubmed.rb	644	2.99 KB	c3160b959f0d89fbc64be4974461341d2ccd14eacd9d4d9c9c97bf62498522b9
sample/demo_targetp_report.rb	644	3.27 KB	29e1c7c9fa0b3bf213064bafb5d586133e6469196e3658aaa8e6fe0f5148cf82
sample/enzymes.rb	755	2 KB	6e6056acba8725e95dd245dc889c3f5d388001b0111923bc973edb6600fecb53
sample/fastagrep.rb	755	1.78 KB	cb2f5248e1106048f2428cef80577fbab52ec65ee81ae33dbfb5de02ee90ecbb
sample/fastasort.rb	755	1.75 KB	1b62217e8944bd9815b230caadb3665dd82d70885ef67643795c21e616a8a831
sample/genes2nuc.rb	755	955 Bytes	0caf11a1a36cc66aa4dfcf92ff53af12ce4990b663a2096d907243b736b67267
sample/genes2pep.rb	755	955 Bytes	c8e66040931bfaf471485d02057b6f1efb407805045541cd7152ada2bc11860a
sample/goslim.rb	755	6.62 KB	f88251ccd40a5548b5b1fa9e6515732282f53a3819185afb67b78b4b69991f14
sample/gt2fasta.rb	755	1.19 KB	a2276c062324475448793430ead285622080fba27cd386fbdef8008218a5a727
sample/pmsearch.rb	755	1.32 KB	485c955f5493b3056e13c335572cde72f9f676ae80a2a70b06b7f22a3d1e3422
sample/test_phyloxml_big.rb	644	5.93 KB	fd6a5a8c459d8eed7ede672216c807c073459d824dd0606fed06ca0dbe1f29e3
sample/tfastx2tab.rb	755	2.39 KB	166ff75261d96454f297b3986dd16a154baeb5be15684be68871ba147e73ee87
test/data/HMMER/hmmsearch.out	644	3.67 KB	575ce8e79d16903c9cf7670748e88bad399066ef5b9bb35f93cb36298d76b8f9
test/data/KEGG/D00063.drug	644	3.92 KB	d7941a74bd701f93ab057f6e4ab21cd043d7e53c4885a85be8d352f7329df3d8
test/data/KEGG/G01366.glycan	644	545 Bytes	e103e8ecab1b285dd603215f6ce8a30e8fc7ca3f625c01967b7c5a4029bd42c7
test/data/blast/b0002.faa	644	1.02 KB	bfd37a1019479f9388ea3c0151097176337d608993f0d0d1b6e0c69ef7850c3b
test/data/embl/AB090716.embl	644	2.47 KB	0cf0a12b44f6472a021abcf4dc38f2f8a64d6dd4049463056057968e2ce0f0f4
test/data/embl/AB090716.embl.rel89	644	2.49 KB	ac5f6d55a30fc5f050f0d8ab1f50fb206707385e7b8434daf02dd7ed623f55a0
test/data/fasta/example1.txt	644	4.66 KB	7b441d36bd74e2bb8662c58aee4fd9003efe79a59eb0449558f4855d839c3bf8
test/data/fasta/example2.txt	644	1.35 KB	228e65bbb2986163fae76f27c57f046d0b3bc3f76cabd0f9f8dc65e6ad31460a
test/data/fastq/error_diff_ids.fastq	644	608 Bytes	fb28be12cda772adc2ca0d29c7b1159b439472ad8383406b2be512249bda347e
test/data/fastq/error_double_seq.fastq	644	669 Bytes	14b7fdfed604a3eb005d03cbe11d419cdccf81426bf6de1930fc06bf934dbd14
test/data/fastq/error_long_qual.fastq	644	609 Bytes	4649efbe152fcc28e1c39b2721ce52f147252a7ee0b55ceb22d535dae1277d48
test/data/fastq/error_qual_del.fastq	644	608 Bytes	843acd2731c024662a481a9ff87349f4372cb407850fdd1e1b6d1c1dcc72de54
test/data/fastq/error_qual_escape.fastq	644	608 Bytes	12659079d3d9f9348990d3c540988d3dd21dd80a5abebbe9527b5a24eb2a3e2c
test/data/fastq/error_qual_null.fastq	644	610 Bytes	72af9fe18e7f35688f717b685771f6da3fb1534d54f3af0437be97ecf4c617eb
test/data/fastq/error_qual_vtab.fastq	644	608 Bytes	24629e256f3ad949817c8e0c1f5e117c1d62fc64b96d74fa0b9ffb9a52b56274
test/data/fastq/error_short_qual.fastq	644	607 Bytes	f92205c3a8e15c4cb233fd3de4876f2ef0d34ab5693db30a9da6149bcdebe0dd
test/data/fastq/error_spaces.fastq	644	628 Bytes	478e3f6c09d4f4ac82b68b3607c7d5860fb0c3192b7f04772694067301e6e767
test/data/fastq/error_trunc_in_title.fastq	644	513 Bytes	15592000903ec62f12a22835bd0194e85b1c40ead8732c70e6f95e265c74db33
test/data/fastq/illumina_full_range_as_sanger.fastq	644	426 Bytes	4148a8f6ae111de3d10933e1055dadb932e6f93926f75cf3983d36646fe37e90
test/data/fastq/illumina_full_range_as_solexa.fastq	644	426 Bytes	8c7499a7f6dc5a0c6a2a8af7c5051e6c47dbc10bf106e721db50e40634925a5d
test/data/fastq/illumina_full_range_original_illumina.fastq	644	426 Bytes	dc2cbaea780de049b285d2b13c0f9a7cb270f7e493a2233b9846060b56ca3e77
test/data/fastq/longreads_as_illumina.fastq	644	8.19 KB	3be788dd8a50564cb7b2bdddd3005c41dc85ec866242f8979d1223b97f370447
test/data/fastq/longreads_as_sanger.fastq	644	8.19 KB	9b1f6ac49d2a2bfc60170ac1edf5a772a3bfa1dd9d731d4f36524f6c7f9321f6
test/data/fastq/misc_dna_as_illumina.fastq	644	767 Bytes	8c059e0f208320e2443ff5ae1f5c6c2be741a38f48caaf967c269ae264b35a28
test/data/fastq/misc_dna_as_sanger.fastq	644	767 Bytes	56d7fb3045c6f0ef3e2a4e35c4e4ccca79674c4a561e4e5f70a164e0d2393f51
test/data/fastq/misc_dna_original_sanger.fastq	644	767 Bytes	56d7fb3045c6f0ef3e2a4e35c4e4ccca79674c4a561e4e5f70a164e0d2393f51
test/data/fastq/misc_rna_as_illumina.fastq	644	774 Bytes	8c421caeb94ff3a46da42307e67f8ad21ef02763793f2a695872651e2b203635
test/data/fastq/misc_rna_original_sanger.fastq	644	774 Bytes	b50686397fc812ecf7c726901acc1f127be1d29dcb6039bf35970e378ba51893
test/data/fastq/sanger_full_range_original_sanger.fastq	644	550 Bytes	daa8500ee0d0b8242c65991f4965b1ec445cf9f57565b838d3ba760e5313cb00
test/data/fastq/solexa_full_range_as_sanger.fastq	644	450 Bytes	10b0c1a68a40b726229f23f0989637e6479513965bb9c450ac81eee1ce796808
test/data/fastq/solexa_full_range_as_solexa.fastq	644	450 Bytes	e6c95762306bf1cbfd7bb952215fc20751caf2448c083f6fdf4414dc8f96e8c1
test/data/fastq/solexa_full_range_original_solexa.fastq	644	450 Bytes	e6c95762306bf1cbfd7bb952215fc20751caf2448c083f6fdf4414dc8f96e8c1
test/data/fastq/wrapping_original_sanger.fastq	644	975 Bytes	6f692d81aad84c258e0dc42c6ca8dcf7b7da694c177a3e948820dd1ffb6e017a
test/data/iprscan/merged.txt	644	5.17 KB	b8920e4a017e8c9d0bdd837bf6691c8ed13fe3dfad8f5992b97cdb1f4db62b8c
test/data/meme/mast	644	0 Bytes	e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
test/data/meme/meme.out	644	190 Bytes	42d3f2d71843fb9cbc0a9d3b3db6e2e17655f06bfa0a2694c814eeafeb49fde0
test/data/paml/codeml/output.txt	644	5.47 KB	aa4dfcbc3cbbf663558c2129d338285ca1d541a29ad0104c55765b552bfdb3f5
test/data/paml/codeml/rates	644	7.41 KB	613b284a3821ed6c1cc2f6f03db46b509cb045ac45763fe66e1ca7c0b15af081
test/data/refseq/nm_126355.entret	644	3.4 KB	60a6bdd9418cc8b9bfc96a1017f412db4f6baddfb3bd9a33c17297bbfc89aee7
test/data/sanger_chromatogram/test_chromatogram_abif.ab1	644	223 KB	8dcd2b30c70cc4ca455868b9f0df5dc588c54ff0be00066810c11442acd6effc
test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf	644	46.4 KB	db84e92dc2aacbf0d84f003593494292e8799a4677c003f6b7d19ff4abfd0061
test/data/sim4/simple-A4.sim4	644	661 Bytes	ab1a4c389192697f64269ca4af532edd7ee94977ef0ca5c64694bef727bb6768
test/data/uniprot/p53_human.uniprot	644	71 KB	cf6237bed4c283ab5a40c330c6554d49a1ab52f48069cfd90f3082edfde2ea98
test/functional/bio/io/test_togows.rb	644	6.78 KB	f14f59a0b1f87cf5dc51e26feb4365483690f4827814cb52df0a0bc82a612af4
test/functional/bio/test_command.rb	644	9.17 KB	f11f26094eee513aa0133f13488f6dd59b24ec7da95a43a461e2c2c7f32891d1
test/runner.rb	644	893 Bytes	994623525809720283ca1248ce58d5982f838d3f42ea17bc6adcf8c18c435b7c
test/unit/bio/appl/blast/test_report.rb	644	33.6 KB	89b8628294d8c95a1ee03e53aceeaa9170e4b5cd0e4fc405c7be6c5e4d088b98
test/unit/bio/appl/genscan/test_report.rb	644	4.84 KB	62107663287c7a4d74b63b64f1ee1d85d9269b4caf5ed27efd32dcd209050b22
test/unit/bio/appl/hmmer/test_report.rb	644	8.51 KB	8388e84f4c6e92898daa0e3e186247d42022c4415d51a157685c36750c044bcd
test/unit/bio/appl/meme/mast/test_report.rb	644	1.15 KB	33e2f7b746315e46468e66a0e59bf83f323eca9cc935a4c85a146f00a3d4b0b3
test/unit/bio/appl/sim4/test_report.rb	644	21.4 KB	c19a66d6d6196a357be8bd692e64d542bb9a63d9ac01df575a770640d72eb201
test/unit/bio/appl/targetp/test_report.rb	644	3.72 KB	9d97b77415866f5cf4bff800c16ac6b4aef5ee0cc331366af18511b383198476
test/unit/bio/appl/test_pts1.rb	644	1.75 KB	646eecf9f286f7eeed968357376f2ec18b2b6313bb6a7da7373f6a9ef94f5e31
test/unit/bio/data/test_aa.rb	644	1.86 KB	2c800117a296a02a2a23a4677c830dffc5fd5e0233d2d97fbaf43ef71fca5b92
test/unit/bio/data/test_codontable.rb	644	2.32 KB	7cda469bbeb6e38b0efc78aba38672493332ed436f4302feb79e8ba5ff18d3b6
test/unit/bio/data/test_na.rb	644	1.84 KB	ea6f5fc59305bddc08aa06a7c327a3c8b6e0f421e860397d4270b1129407b168
test/unit/bio/db/embl/test_embl_rel89.rb	644	4.97 KB	729b4b317e26d6c3f63291037b8df001f6521e27ee9a61f54ed9d1daebb9ba7b
test/unit/bio/db/embl/test_sptr.rb	644	80 KB	3560b08f565db56408cb57eae84db5d5475b2fd9d18f55afa89c7efac0540ab6
test/unit/bio/db/embl/test_uniprot.rb	644	754 Bytes	4a1a85b00ef7bbaee0a2f7da34e76d714983db5ca43810d23882dc8c614cf253
test/unit/bio/db/fasta/test_format_qual.rb	644	12.3 KB	b4cbaf41abba7674ef51a9f804edb2ea74d1783a09bf292d9831a3c6273e5a2b
test/unit/bio/db/kegg/test_compound.rb	644	7.86 KB	890fb8731a62a2819b41fb93a374cd9039007a1bd4397c75a0e5db028c1d4bbb
test/unit/bio/db/pdb/test_pdb.rb	644	3.36 KB	e34e99f26e2f0325fd459e8d02cd4f8b822494adec2e93ea569189384cbe294c
test/unit/bio/db/sanger_chromatogram/test_abif.rb	644	3.48 KB	9f4177e17a0b065f7a151e4d459e157b0420b9ae6b0ef4c10b91f87ecf7dd187
test/unit/bio/db/test_aaindex.rb	644	5.94 KB	3ba1423b35b046545b5076f8919cc4562339c26f85eb51ac5ddb30f6c1a4a292
test/unit/bio/db/test_qual.rb	644	1.43 KB	1984a9ce92ddbf7d823f685cda054c044d59a4efc2304925a0bcd81694b19dea
test/unit/bio/db/test_rebase.rb	644	2.5 KB	ba61c71f56f55add6307d6ed0aaf465153051394e17d1bb5abb03a246838c861
test/unit/bio/io/flatfile/test_autodetection.rb	644	10.1 KB	b672edf6c8f2d025e0000aab649e42457d69dba5b34a604ec7a246ef8c91c731
test/unit/bio/io/test_ddbjxml.rb	644	2.3 KB	3a9cefebea194d7b6135694b0d0cd516dfe68b40bbb894aa684fc93a8ce0f690
test/unit/bio/io/test_flatfile.rb	644	12.9 KB	cf5883c0606271c205719b03f62cbf7d69f2df717622ad2b7c8a7a9177b57d39
test/unit/bio/sequence/test_quality_score.rb	644	12.2 KB	c9d802fcfb641e7173a2f51717ca369376aa81b8a37170af7e09e10f453eebff
test/unit/bio/test_alignment.rb	644	34 KB	02dc9f584730ae7aa7d43a51b8526c2946f442c557025ff97144aee0b46634f3
test/unit/bio/test_command.rb	644	11.1 KB	674a257fe65bb56120245bd0260c236f17f74aa468a3485171eab79ff0df281d
test/unit/bio/test_feature.rb	644	3.16 KB	113c5a97d4acd60782dd8f9f29522c34673ae4001600ef1a2b6aadc41d1fc675
test/unit/bio/test_map.rb	644	8.1 KB	609d4551a3506a90e086c24b1daeff3a34762bca796640213f4aea7e5916586f
test/unit/bio/test_reference.rb	644	7.01 KB	15bc562911c11944ab03a8186a0e1c532e7633269df4fde80ce871dd68eba22d
test/unit/bio/test_sequence.rb	644	9.25 KB	2483b6761d1e0bca4ea5db600d98a35b5dc9c2a8d119032501545f27aac21a28
test/unit/bio/test_tree.rb	644	18.7 KB	51ee11721f58d20847a2b2da7b704be068e692f2056b2fe70506a4f8c7ffb1c3
test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb	644	3.45 KB	ba6116356af552be39457a0aee054aaf529774d8c905da6ee399141fe6ad335a
test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb	644	7.7 KB	efadc0c9037ad1205c09a1a8177cf60f3a59f45eea852a1892698bb69d741e6b
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb	644	2.2 KB	dd35fc665ed061594953f2a98495febde2b1cf9a53c927a096d94af1c2b96f68
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb	644	3.12 KB	e0e643a36525596fa30b8c4d5831ebdd4d5a3dc3ccf1df72281abfeaeea06a56
test/unit/bio/util/restriction_enzyme/test_single_strand.rb	644	5.02 KB	9b3348b3e537492f8558b4d66c743dff875e19480942c37ea8f2036ca6c17d3a
test/unit/bio/util/restriction_enzyme/test_string_formatting.rb	644	1.75 KB	e200dbd83a5a573706039647aec09795c47ae71089a0796808c8fb232e015238
test/unit/bio/util/test_restriction_enzyme.rb	644	1.16 KB	facfeed8a4ac8a8003d6111185dd88b31a87416e39c6e177b22e69d674ebaf97