wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
@@ -0,0 +1,15 @@
|
|
1
|
+
>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)
|
2
|
+
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
|
3
|
+
LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
|
4
|
+
ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
|
5
|
+
ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
|
6
|
+
PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
|
7
|
+
EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
|
8
|
+
CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
|
9
|
+
ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL
|
10
|
+
LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
|
11
|
+
VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
|
12
|
+
RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
|
13
|
+
REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
|
14
|
+
NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
|
15
|
+
YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
|
@@ -0,0 +1,128 @@
|
|
1
|
+
BLASTP 2.2.10 [Oct-19-2004]
|
2
|
+
|
3
|
+
|
4
|
+
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
|
5
|
+
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
|
6
|
+
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
|
7
|
+
programs", Nucleic Acids Res. 25:3389-3402.
|
8
|
+
|
9
|
+
Query= eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional:
|
10
|
+
aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal)
|
11
|
+
[EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928
|
12
|
+
aspartate kinase (A)
|
13
|
+
(820 letters)
|
14
|
+
|
15
|
+
Database: b0002.faa
|
16
|
+
1 sequences; 820 total letters
|
17
|
+
|
18
|
+
Searching.done
|
19
|
+
|
20
|
+
Score E
|
21
|
+
Sequences producing significant alignments: (bits) Value
|
22
|
+
|
23
|
+
eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokin... 1567 0.0
|
24
|
+
|
25
|
+
>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase
|
26
|
+
I (N-terminal); homoserine dehydrogenase I (C-terminal)
|
27
|
+
[EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase;
|
28
|
+
K00928 aspartate kinase (A)
|
29
|
+
Length = 820
|
30
|
+
|
31
|
+
Score = 1567 bits (4058), Expect = 0.0
|
32
|
+
Identities = 806/820 (98%), Positives = 806/820 (98%)
|
33
|
+
|
34
|
+
Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
|
35
|
+
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
|
36
|
+
Sbjct: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
|
37
|
+
|
38
|
+
Query: 61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
|
39
|
+
LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
|
40
|
+
Sbjct: 61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
|
41
|
+
|
42
|
+
Query: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
|
43
|
+
ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
|
44
|
+
Sbjct: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
|
45
|
+
|
46
|
+
Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
|
47
|
+
ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
|
48
|
+
Sbjct: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
|
49
|
+
|
50
|
+
Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
|
51
|
+
PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
|
52
|
+
Sbjct: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
|
53
|
+
|
54
|
+
Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
|
55
|
+
EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
|
56
|
+
Sbjct: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
|
57
|
+
|
58
|
+
Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
|
59
|
+
CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
|
60
|
+
Sbjct: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
|
61
|
+
|
62
|
+
Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQXXXXXXXXXXXXXXAL 480
|
63
|
+
ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQ AL
|
64
|
+
Sbjct: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480
|
65
|
+
|
66
|
+
Query: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
|
67
|
+
LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
|
68
|
+
Sbjct: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
|
69
|
+
|
70
|
+
Query: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
|
71
|
+
VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
|
72
|
+
Sbjct: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
|
73
|
+
|
74
|
+
Query: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
|
75
|
+
RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
|
76
|
+
Sbjct: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
|
77
|
+
|
78
|
+
Query: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
|
79
|
+
REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
|
80
|
+
Sbjct: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
|
81
|
+
|
82
|
+
Query: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
|
83
|
+
NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
|
84
|
+
Sbjct: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
|
85
|
+
|
86
|
+
Query: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
|
87
|
+
YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
|
88
|
+
Sbjct: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
|
89
|
+
|
90
|
+
|
91
|
+
Database: b0002.faa
|
92
|
+
Posted date: Aug 7, 2005 7:29 AM
|
93
|
+
Number of letters in database: 820
|
94
|
+
Number of sequences in database: 1
|
95
|
+
|
96
|
+
Lambda K H
|
97
|
+
0.319 0.134 0.383
|
98
|
+
|
99
|
+
Gapped
|
100
|
+
Lambda K H
|
101
|
+
0.267 0.0410 0.140
|
102
|
+
|
103
|
+
|
104
|
+
Matrix: BLOSUM62
|
105
|
+
Gap Penalties: Existence: 11, Extension: 1
|
106
|
+
Number of Hits to DB: 1986
|
107
|
+
Number of Sequences: 1
|
108
|
+
Number of extensions: 52
|
109
|
+
Number of successful extensions: 8
|
110
|
+
Number of sequences better than 10.0: 1
|
111
|
+
Number of HSP's better than 10.0 without gapping: 1
|
112
|
+
Number of HSP's successfully gapped in prelim test: 0
|
113
|
+
Number of HSP's that attempted gapping in prelim test: 0
|
114
|
+
Number of HSP's gapped (non-prelim): 1
|
115
|
+
length of query: 820
|
116
|
+
length of database: 820
|
117
|
+
effective HSP length: 42
|
118
|
+
effective length of query: 778
|
119
|
+
effective length of database: 778
|
120
|
+
effective search space: 605284
|
121
|
+
effective search space used: 605284
|
122
|
+
T: 11
|
123
|
+
A: 40
|
124
|
+
X1: 16 ( 7.4 bits)
|
125
|
+
X2: 38 (14.6 bits)
|
126
|
+
X3: 64 (24.7 bits)
|
127
|
+
S1: 30 (16.7 bits)
|
128
|
+
S2: 30 (16.2 bits)
|
@@ -0,0 +1,65 @@
|
|
1
|
+
<?xml version="1.0"?>
|
2
|
+
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
|
3
|
+
<BlastOutput>
|
4
|
+
<BlastOutput_program>blastp</BlastOutput_program>
|
5
|
+
<BlastOutput_version>blastp 2.2.10 [Oct-19-2004]</BlastOutput_version>
|
6
|
+
<BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
|
7
|
+
<BlastOutput_db>b0002.faa</BlastOutput_db>
|
8
|
+
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
|
9
|
+
<BlastOutput_query-def>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)</BlastOutput_query-def>
|
10
|
+
<BlastOutput_query-len>820</BlastOutput_query-len>
|
11
|
+
<BlastOutput_param>
|
12
|
+
<Parameters>
|
13
|
+
<Parameters_matrix>BLOSUM62</Parameters_matrix>
|
14
|
+
<Parameters_expect>10</Parameters_expect>
|
15
|
+
<Parameters_gap-open>11</Parameters_gap-open>
|
16
|
+
<Parameters_gap-extend>1</Parameters_gap-extend>
|
17
|
+
<Parameters_filter>S</Parameters_filter>
|
18
|
+
</Parameters>
|
19
|
+
</BlastOutput_param>
|
20
|
+
<BlastOutput_iterations>
|
21
|
+
<Iteration>
|
22
|
+
<Iteration_iter-num>1</Iteration_iter-num>
|
23
|
+
<Iteration_hits>
|
24
|
+
<Hit>
|
25
|
+
<Hit_num>1</Hit_num>
|
26
|
+
<Hit_id>gnl|BL_ORD_ID|0</Hit_id>
|
27
|
+
<Hit_def>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)</Hit_def>
|
28
|
+
<Hit_accession>0</Hit_accession>
|
29
|
+
<Hit_len>820</Hit_len>
|
30
|
+
<Hit_hsps>
|
31
|
+
<Hsp>
|
32
|
+
<Hsp_num>1</Hsp_num>
|
33
|
+
<Hsp_bit-score>1567.75</Hsp_bit-score>
|
34
|
+
<Hsp_score>4058</Hsp_score>
|
35
|
+
<Hsp_evalue>0</Hsp_evalue>
|
36
|
+
<Hsp_query-from>1</Hsp_query-from>
|
37
|
+
<Hsp_query-to>820</Hsp_query-to>
|
38
|
+
<Hsp_hit-from>1</Hsp_hit-from>
|
39
|
+
<Hsp_hit-to>820</Hsp_hit-to>
|
40
|
+
<Hsp_query-frame>1</Hsp_query-frame>
|
41
|
+
<Hsp_hit-frame>1</Hsp_hit-frame>
|
42
|
+
<Hsp_identity>820</Hsp_identity>
|
43
|
+
<Hsp_positive>820</Hsp_positive>
|
44
|
+
<Hsp_align-len>820</Hsp_align-len>
|
45
|
+
<Hsp_qseq>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_qseq>
|
46
|
+
<Hsp_hseq>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_hseq>
|
47
|
+
<Hsp_midline>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_midline>
|
48
|
+
</Hsp>
|
49
|
+
</Hit_hsps>
|
50
|
+
</Hit>
|
51
|
+
</Iteration_hits>
|
52
|
+
<Iteration_stat>
|
53
|
+
<Statistics>
|
54
|
+
<Statistics_db-num>1</Statistics_db-num>
|
55
|
+
<Statistics_db-len>820</Statistics_db-len>
|
56
|
+
<Statistics_hsp-len>42</Statistics_hsp-len>
|
57
|
+
<Statistics_eff-space>605284</Statistics_eff-space>
|
58
|
+
<Statistics_kappa>0.041</Statistics_kappa>
|
59
|
+
<Statistics_lambda>0.267</Statistics_lambda>
|
60
|
+
<Statistics_entropy>0.14</Statistics_entropy>
|
61
|
+
</Statistics>
|
62
|
+
</Iteration_stat>
|
63
|
+
</Iteration>
|
64
|
+
</BlastOutput_iterations>
|
65
|
+
</BlastOutput>
|
@@ -0,0 +1 @@
|
|
1
|
+
eco:b0002 eco:b0002 100.00 820 0 0 1 820 1 820 0.0 1567
|
@@ -0,0 +1,188 @@
|
|
1
|
+
<?xml version="1.0"?>
|
2
|
+
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
|
3
|
+
<BlastOutput>
|
4
|
+
<BlastOutput_program>blastp</BlastOutput_program>
|
5
|
+
<BlastOutput_version>blastp 2.2.18 [Mar-02-2008]</BlastOutput_version>
|
6
|
+
<BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
|
7
|
+
<BlastOutput_db>BA000007.faa</BlastOutput_db>
|
8
|
+
<BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID>
|
9
|
+
<BlastOutput_query-def>gi|1790845|gb|AAC77338.1| predicted DNA-binding transcriptional regulator [Escherichia coli str. K-12 substr. MG1655]</BlastOutput_query-def>
|
10
|
+
<BlastOutput_query-len>443</BlastOutput_query-len>
|
11
|
+
<BlastOutput_param>
|
12
|
+
<Parameters>
|
13
|
+
<Parameters_matrix>BLOSUM62</Parameters_matrix>
|
14
|
+
<Parameters_expect>0.001</Parameters_expect>
|
15
|
+
<Parameters_gap-open>11</Parameters_gap-open>
|
16
|
+
<Parameters_gap-extend>1</Parameters_gap-extend>
|
17
|
+
<Parameters_filter>F</Parameters_filter>
|
18
|
+
</Parameters>
|
19
|
+
</BlastOutput_param>
|
20
|
+
<BlastOutput_iterations>
|
21
|
+
<Iteration>
|
22
|
+
<Iteration_iter-num>2</Iteration_iter-num>
|
23
|
+
<Iteration_query-ID>lcl|2_0</Iteration_query-ID>
|
24
|
+
<Iteration_query-def>gi|1790846|gb|AAC77339.1| lipoate-protein ligase A [Escherichia coli str. K-12</Iteration_query-def>
|
25
|
+
<Iteration_query-len>346</Iteration_query-len>
|
26
|
+
<Iteration_hits>
|
27
|
+
<Hit>
|
28
|
+
<Hit_num>1</Hit_num>
|
29
|
+
<Hit_id>gi|13364823|dbj|BAB38768.1|</Hit_id>
|
30
|
+
<Hit_def>putative lipoate-protein ligase A [Escherichia coli O157:H7 str. Sakai]</Hit_def>
|
31
|
+
<Hit_accession>BAB38768</Hit_accession>
|
32
|
+
<Hit_len>562</Hit_len>
|
33
|
+
<Hit_hsps>
|
34
|
+
<Hsp>
|
35
|
+
<Hsp_num>1</Hsp_num>
|
36
|
+
<Hsp_bit-score>697.197</Hsp_bit-score>
|
37
|
+
<Hsp_score>1798</Hsp_score>
|
38
|
+
<Hsp_evalue>0</Hsp_evalue>
|
39
|
+
<Hsp_query-from>9</Hsp_query-from>
|
40
|
+
<Hsp_query-to>346</Hsp_query-to>
|
41
|
+
<Hsp_hit-from>225</Hsp_hit-from>
|
42
|
+
<Hsp_hit-to>562</Hsp_hit-to>
|
43
|
+
<Hsp_query-frame>1</Hsp_query-frame>
|
44
|
+
<Hsp_hit-frame>1</Hsp_hit-frame>
|
45
|
+
<Hsp_identity>331</Hsp_identity>
|
46
|
+
<Hsp_positive>335</Hsp_positive>
|
47
|
+
<Hsp_align-len>338</Hsp_align-len>
|
48
|
+
<Hsp_qseq>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR</Hsp_qseq>
|
49
|
+
<Hsp_hseq>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTAEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGIPHEQVCEAITEAFFAHYGERVEAEIISPDKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFSWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPDQEKELRELSTWIAGAVR</Hsp_hseq>
|
50
|
+
<Hsp_midline>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKT EGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGI HEQVCEAITEAFFAHYGERVEAEIISP+KTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERF+WGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFP+QEKELRELS W+AGAVR</Hsp_midline>
|
51
|
+
</Hsp>
|
52
|
+
</Hit_hsps>
|
53
|
+
</Hit>
|
54
|
+
</Iteration_hits>
|
55
|
+
<Iteration_stat>
|
56
|
+
<Statistics>
|
57
|
+
<Statistics_db-num>5361</Statistics_db-num>
|
58
|
+
<Statistics_db-len>1609188</Statistics_db-len>
|
59
|
+
<Statistics_hsp-len>0</Statistics_hsp-len>
|
60
|
+
<Statistics_eff-space>0</Statistics_eff-space>
|
61
|
+
<Statistics_kappa>0.041</Statistics_kappa>
|
62
|
+
<Statistics_lambda>0.267</Statistics_lambda>
|
63
|
+
<Statistics_entropy>0.14</Statistics_entropy>
|
64
|
+
</Statistics>
|
65
|
+
</Iteration_stat>
|
66
|
+
</Iteration>
|
67
|
+
<Iteration>
|
68
|
+
<Iteration_iter-num>3</Iteration_iter-num>
|
69
|
+
<Iteration_query-ID>lcl|3_0</Iteration_query-ID>
|
70
|
+
<Iteration_query-def>gi|1790847|gb|AAC77340.1| conserved protein [Escherichia coli str. K-12 substr. MG1655]</Iteration_query-def>
|
71
|
+
<Iteration_query-len>214</Iteration_query-len>
|
72
|
+
<Iteration_hits>
|
73
|
+
<Hit>
|
74
|
+
<Hit_num>1</Hit_num>
|
75
|
+
<Hit_id>gi|13364823|dbj|BAB38768.1|</Hit_id>
|
76
|
+
<Hit_def>putative lipoate-protein ligase A [Escherichia coli O157:H7 str. Sakai]</Hit_def>
|
77
|
+
<Hit_accession>BAB38768</Hit_accession>
|
78
|
+
<Hit_len>562</Hit_len>
|
79
|
+
<Hit_hsps>
|
80
|
+
<Hsp>
|
81
|
+
<Hsp_num>1</Hsp_num>
|
82
|
+
<Hsp_bit-score>432.95</Hsp_bit-score>
|
83
|
+
<Hsp_score>1112</Hsp_score>
|
84
|
+
<Hsp_evalue>7.66702e-123</Hsp_evalue>
|
85
|
+
<Hsp_query-from>1</Hsp_query-from>
|
86
|
+
<Hsp_query-to>214</Hsp_query-to>
|
87
|
+
<Hsp_hit-from>1</Hsp_hit-from>
|
88
|
+
<Hsp_hit-to>214</Hsp_hit-to>
|
89
|
+
<Hsp_query-frame>1</Hsp_query-frame>
|
90
|
+
<Hsp_hit-frame>1</Hsp_hit-frame>
|
91
|
+
<Hsp_identity>214</Hsp_identity>
|
92
|
+
<Hsp_positive>214</Hsp_positive>
|
93
|
+
<Hsp_align-len>214</Hsp_align-len>
|
94
|
+
<Hsp_qseq>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_qseq>
|
95
|
+
<Hsp_hseq>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_hseq>
|
96
|
+
<Hsp_midline>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_midline>
|
97
|
+
</Hsp>
|
98
|
+
</Hit_hsps>
|
99
|
+
</Hit>
|
100
|
+
</Iteration_hits>
|
101
|
+
<Iteration_stat>
|
102
|
+
<Statistics>
|
103
|
+
<Statistics_db-num>5361</Statistics_db-num>
|
104
|
+
<Statistics_db-len>1609188</Statistics_db-len>
|
105
|
+
<Statistics_hsp-len>0</Statistics_hsp-len>
|
106
|
+
<Statistics_eff-space>0</Statistics_eff-space>
|
107
|
+
<Statistics_kappa>0.041</Statistics_kappa>
|
108
|
+
<Statistics_lambda>0.267</Statistics_lambda>
|
109
|
+
<Statistics_entropy>0.14</Statistics_entropy>
|
110
|
+
</Statistics>
|
111
|
+
</Iteration_stat>
|
112
|
+
</Iteration>
|
113
|
+
<Iteration>
|
114
|
+
<Iteration_iter-num>5</Iteration_iter-num>
|
115
|
+
<Iteration_query-ID>lcl|5_0</Iteration_query-ID>
|
116
|
+
<Iteration_query-def>gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]</Iteration_query-def>
|
117
|
+
<Iteration_query-len>322</Iteration_query-len>
|
118
|
+
<Iteration_hits>
|
119
|
+
<Hit>
|
120
|
+
<Hit_num>1</Hit_num>
|
121
|
+
<Hit_id>gi|13364824|dbj|BAB38769.1|</Hit_id>
|
122
|
+
<Hit_def>3-phosphoserine phosphatase [Escherichia coli O157:H7 str. Sakai]</Hit_def>
|
123
|
+
<Hit_accession>BAB38769</Hit_accession>
|
124
|
+
<Hit_len>322</Hit_len>
|
125
|
+
<Hit_hsps>
|
126
|
+
<Hsp>
|
127
|
+
<Hsp_num>1</Hsp_num>
|
128
|
+
<Hsp_bit-score>657.907</Hsp_bit-score>
|
129
|
+
<Hsp_score>1696</Hsp_score>
|
130
|
+
<Hsp_evalue>0</Hsp_evalue>
|
131
|
+
<Hsp_query-from>1</Hsp_query-from>
|
132
|
+
<Hsp_query-to>322</Hsp_query-to>
|
133
|
+
<Hsp_hit-from>1</Hsp_hit-from>
|
134
|
+
<Hsp_hit-to>322</Hsp_hit-to>
|
135
|
+
<Hsp_query-frame>1</Hsp_query-frame>
|
136
|
+
<Hsp_hit-frame>1</Hsp_hit-frame>
|
137
|
+
<Hsp_identity>322</Hsp_identity>
|
138
|
+
<Hsp_positive>322</Hsp_positive>
|
139
|
+
<Hsp_align-len>322</Hsp_align-len>
|
140
|
+
<Hsp_qseq>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_qseq>
|
141
|
+
<Hsp_hseq>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_hseq>
|
142
|
+
<Hsp_midline>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_midline>
|
143
|
+
</Hsp>
|
144
|
+
</Hit_hsps>
|
145
|
+
</Hit>
|
146
|
+
<Hit>
|
147
|
+
<Hit_num>2</Hit_num>
|
148
|
+
<Hit_id>gi|13363792|dbj|BAB37741.1|</Hit_id>
|
149
|
+
<Hit_def>zinc-transporting ATPase [Escherichia coli O157:H7 str. Sakai]</Hit_def>
|
150
|
+
<Hit_accession>BAB37741</Hit_accession>
|
151
|
+
<Hit_len>732</Hit_len>
|
152
|
+
<Hit_hsps>
|
153
|
+
<Hsp>
|
154
|
+
<Hsp_num>1</Hsp_num>
|
155
|
+
<Hsp_bit-score>38.1206</Hsp_bit-score>
|
156
|
+
<Hsp_score>87</Hsp_score>
|
157
|
+
<Hsp_evalue>0.000899657</Hsp_evalue>
|
158
|
+
<Hsp_query-from>190</Hsp_query-from>
|
159
|
+
<Hsp_query-to>311</Hsp_query-to>
|
160
|
+
<Hsp_hit-from>569</Hsp_hit-from>
|
161
|
+
<Hsp_hit-to>668</Hsp_hit-to>
|
162
|
+
<Hsp_query-frame>1</Hsp_query-frame>
|
163
|
+
<Hsp_hit-frame>1</Hsp_hit-frame>
|
164
|
+
<Hsp_identity>39</Hsp_identity>
|
165
|
+
<Hsp_positive>56</Hsp_positive>
|
166
|
+
<Hsp_gaps>24</Hsp_gaps>
|
167
|
+
<Hsp_align-len>123</Hsp_align-len>
|
168
|
+
<Hsp_qseq>VLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVN-EKAEVTIRHADLMGV</Hsp_qseq>
|
169
|
+
<Hsp_hseq>ISELNALGVKGVILTG----------DNPRAAAAIAGELGL---EFKAGLL-----PEDKVKAVTELNQHA--PLAM---VGDGINDAPAMKAAAIGIAMGSGTDVALETADAALTHNHLRGL</Hsp_hseq>
|
170
|
+
<Hsp_midline>+ +L LG K I +G D R A +A EL + +F ++ + K K +T L Q PLA +GDG ND P +KAA +GIA + V E A+ + H L G+</Hsp_midline>
|
171
|
+
</Hsp>
|
172
|
+
</Hit_hsps>
|
173
|
+
</Hit>
|
174
|
+
</Iteration_hits>
|
175
|
+
<Iteration_stat>
|
176
|
+
<Statistics>
|
177
|
+
<Statistics_db-num>5361</Statistics_db-num>
|
178
|
+
<Statistics_db-len>1609188</Statistics_db-len>
|
179
|
+
<Statistics_hsp-len>0</Statistics_hsp-len>
|
180
|
+
<Statistics_eff-space>0</Statistics_eff-space>
|
181
|
+
<Statistics_kappa>0.041</Statistics_kappa>
|
182
|
+
<Statistics_lambda>0.267</Statistics_lambda>
|
183
|
+
<Statistics_entropy>0.14</Statistics_entropy>
|
184
|
+
</Statistics>
|
185
|
+
</Iteration_stat>
|
186
|
+
</Iteration>
|
187
|
+
</BlastOutput_iterations>
|
188
|
+
</BlastOutput>
|
@@ -0,0 +1 @@
|
|
1
|
+
@echo %2
|
@@ -0,0 +1,65 @@
|
|
1
|
+
ID AB090716 standard; genomic DNA; VRT; 166 BP.
|
2
|
+
XX
|
3
|
+
AC AB090716;
|
4
|
+
XX
|
5
|
+
SV AB090716.1
|
6
|
+
XX
|
7
|
+
DT 25-OCT-2002 (Rel. 73, Created)
|
8
|
+
DT 29-NOV-2002 (Rel. 73, Last updated, Version 2)
|
9
|
+
XX
|
10
|
+
DE Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive
|
11
|
+
DE opsin, partial cds, specimen_voucher:specimen No. HT-9361.
|
12
|
+
XX
|
13
|
+
KW .
|
14
|
+
XX
|
15
|
+
OS Haplochromis sp. 'muzu, rukwa'
|
16
|
+
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
|
17
|
+
OC Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei;
|
18
|
+
OC Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei;
|
19
|
+
OC Cichlidae; Haplochromis.
|
20
|
+
XX
|
21
|
+
RN [1]
|
22
|
+
RP 1-166
|
23
|
+
RA Terai Y., Mayer W.E., Klein J., Tichy H., Okada N.;
|
24
|
+
RT ;
|
25
|
+
RL Submitted (26-AUG-2002) to the EMBL/GenBank/DDBJ databases.
|
26
|
+
RL Yohey Terai, Tokyo Institute of Technology, Graduate School of Bioscience
|
27
|
+
RL and Biotechnology; 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa
|
28
|
+
RL 226-8501, Japan (E-mail:yterai@bio.titech.ac.jp, Tel:81-45-924-5744,
|
29
|
+
RL Fax:81-45-924-5835)
|
30
|
+
XX
|
31
|
+
RN [2]
|
32
|
+
RX DOI; 10.1073/pnas.232561099.
|
33
|
+
RX MEDLINE; 22342723.
|
34
|
+
RX PUBMED; 12438648.
|
35
|
+
RA Terai Y., Mayer W.E., Klein J., Tichy H., Okada N.;
|
36
|
+
RT "The effect of selection on a long wavelength-sensitive (LWS) opsin gene of
|
37
|
+
RT Lake Victoria cichlid fishes";
|
38
|
+
RL Proc. Natl. Acad. Sci. U.S.A. 99(24):15501-15506(2002).
|
39
|
+
XX
|
40
|
+
FH Key Location/Qualifiers
|
41
|
+
FH
|
42
|
+
FT source 1..166
|
43
|
+
FT /db_xref="taxon:205497"
|
44
|
+
FT /mol_type="genomic DNA"
|
45
|
+
FT /organism="Haplochromis sp. 'muzu, rukwa'"
|
46
|
+
FT /specimen_voucher="specimen No. HT-9361"
|
47
|
+
FT /tissue_type="piece of fin"
|
48
|
+
FT CDS <1..>166
|
49
|
+
FT /codon_start=2
|
50
|
+
FT /db_xref="UniProt/TrEMBL:Q8AUS6"
|
51
|
+
FT /gene="LWS"
|
52
|
+
FT /product="long wavelength-sensitive opsin"
|
53
|
+
FT /protein_id="BAC22028.1"
|
54
|
+
FT /translation="FWPHGLKTSCGPDVFSGSEDPGVQSYMIVLMITCCFIPLAIIILC
|
55
|
+
FT YLAVWMAIRA"
|
56
|
+
FT exon 1..166
|
57
|
+
FT /number=4
|
58
|
+
FT /gene="LWS"
|
59
|
+
FT /product="long wavelength-sensitive opsin"
|
60
|
+
XX
|
61
|
+
SQ Sequence 166 BP; 29 A; 42 C; 41 G; 54 T; 0 other;
|
62
|
+
gttctggcct catggactga agacttcctg tggacctgat gtgttcagtg gaagtgaaga 60
|
63
|
+
ccctggagta cagtcctaca tgattgttct catgattact tgctgtttca tccccctggc 120
|
64
|
+
tatcatcatc ctgtgctacc ttgctgtgtg gatggccatc cgtgct 166
|
65
|
+
//
|