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 +1,63 @@
|
|
1
|
+
ID AB090716; SV 1; linear; genomic DNA; STD; VRT; 166 BP.
|
2
|
+
XX
|
3
|
+
AC AB090716;
|
4
|
+
XX
|
5
|
+
DT 25-OCT-2002 (Rel. 73, Created)
|
6
|
+
DT 14-NOV-2006 (Rel. 89, Last updated, Version 3)
|
7
|
+
XX
|
8
|
+
DE Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive
|
9
|
+
DE opsin, partial cds, specimen_voucher:specimen No. HT-9361.
|
10
|
+
XX
|
11
|
+
KW .
|
12
|
+
XX
|
13
|
+
OS Haplochromis sp. 'muzu, rukwa'
|
14
|
+
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
|
15
|
+
OC Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei;
|
16
|
+
OC Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei;
|
17
|
+
OC Cichlidae; African cichlids; Pseudocrenilabrinae; Haplochromini;
|
18
|
+
OC Haplochromis.
|
19
|
+
XX
|
20
|
+
RN [1]
|
21
|
+
RP 1-166
|
22
|
+
RA Terai Y., Mayer W.E., Klein J., Tichy H., Okada N.;
|
23
|
+
RT ;
|
24
|
+
RL Submitted (26-AUG-2002) to the EMBL/GenBank/DDBJ databases.
|
25
|
+
RL Yohey Terai, Tokyo Institute of Technology, Graduate School of Bioscience
|
26
|
+
RL and Biotechnology; 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa
|
27
|
+
RL 226-8501, Japan (E-mail:yterai@bio.titech.ac.jp, Tel:81-45-924-5744,
|
28
|
+
RL Fax:81-45-924-5835)
|
29
|
+
XX
|
30
|
+
RN [2]
|
31
|
+
RX DOI; 10.1073/pnas.232561099.
|
32
|
+
RX PUBMED; 12438648.
|
33
|
+
RA Terai Y., Mayer W.E., Klein J., Tichy H., Okada N.;
|
34
|
+
RT "The effect of selection on a long wavelength-sensitive (LWS) opsin gene of
|
35
|
+
RT Lake Victoria cichlid fishes";
|
36
|
+
RL Proc. Natl. Acad. Sci. U.S.A. 99(24):15501-15506(2002).
|
37
|
+
XX
|
38
|
+
FH Key Location/Qualifiers
|
39
|
+
FH
|
40
|
+
FT source 1..166
|
41
|
+
FT /organism="Haplochromis sp. 'muzu, rukwa'"
|
42
|
+
FT /mol_type="genomic DNA"
|
43
|
+
FT /specimen_voucher="specimen No. HT-9361"
|
44
|
+
FT /tissue_type="piece of fin"
|
45
|
+
FT /db_xref="taxon:205497"
|
46
|
+
FT CDS <1..>166
|
47
|
+
FT /codon_start=2
|
48
|
+
FT /gene="LWS"
|
49
|
+
FT /product="long wavelength-sensitive opsin"
|
50
|
+
FT /db_xref="UniProtKB/TrEMBL:Q8AUS6"
|
51
|
+
FT /protein_id="BAC22028.1"
|
52
|
+
FT /translation="FWPHGLKTSCGPDVFSGSEDPGVQSYMIVLMITCCFIPLAIIILC
|
53
|
+
FT YLAVWMAIRA"
|
54
|
+
FT exon 1..166
|
55
|
+
FT /gene="LWS"
|
56
|
+
FT /product="long wavelength-sensitive opsin"
|
57
|
+
FT /number=4
|
58
|
+
XX
|
59
|
+
SQ Sequence 166 BP; 29 A; 42 C; 41 G; 54 T; 0 other;
|
60
|
+
gttctggcct catggactga agacttcctg tggacctgat gtgttcagtg gaagtgaaga 60
|
61
|
+
ccctggagta cagtcctaca tgattgttct catgattact tgctgtttca tccccctggc 120
|
62
|
+
tatcatcatc ctgtgctacc ttgctgtgtg gatggccatc cgtgct 166
|
63
|
+
//
|
@@ -0,0 +1,75 @@
|
|
1
|
+
>At1g02580 mRNA (2291 bp) UTR's and CDS
|
2
|
+
aggcgagtggttaatggagaaggaaaaccatgaggacgatggtgagggtttgccacccgaactaaatcagataaaa
|
3
|
+
gagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactc
|
4
|
+
atgcttcacaccatcaatcgtttgacttaaaccagcccgctgcagaggatgataatggaggagacaacaaatcact
|
5
|
+
tttgtcgagaatgcaaaacccacttcgtcatttcagtgcctcatctgattataattcttacgaagatcaaggttat
|
6
|
+
gttcttgatgaggatcaagattatgctcttgaagaagatgtaccattatttcttgatgaagatgtaccattattac
|
7
|
+
caagtgtcaagcttccaattgttgagaagctaccacgatccattacatgggtcttcaccaaaagtagccagctgat
|
8
|
+
ggctgaaagtgattctgtgattggtaagagacaaatctattatttgaatggtgaggcactagaattgagcagtgaa
|
9
|
+
gaagatgaggaagatgaagaagaagatgaggaagaaatcaagaaagaaaaatgcgaattttctgaagatgtagacc
|
10
|
+
gatttatatggacggttgggcaggactatggtttggatgatctggtcgtgcggcgtgctctcgccaagtacctcga
|
11
|
+
agtggatgtttcggacatattggaaagatacaatgaactcaagcttaagaatgatggaactgctggtgaggcttct
|
12
|
+
gatttgacatccaagacaataactactgctttccaggattttgctgatagacgtcattgccgtcgttgcatgatat
|
13
|
+
tcgattgtcatatgcatgagaagtatgagcccgagtctagatccagcgaagacaaatctagtttgtttgaggatga
|
14
|
+
agatagacaaccatgcagtgagcattgttacctcaaggtgaggagtgtgacagaagctgatcatgtgatggataat
|
15
|
+
gataactctatatcaaacaagattgtggtctcagatccaaacaacactatgtggacgcctgtagagaaggatcttt
|
16
|
+
acttgaaaggaattgagatatttgggagaaacagttgtgatgttgcattaaacatacttcgggggcttaagacgtg
|
17
|
+
cctagagatttacaattacatgcgcgaacaagatcaatgtactatgtcattagaccttaacaaaactacacaaaga
|
18
|
+
cacaatcaggttaccaaaaaagtatctcgaaaaagtagtaggtcggtccgcaaaaaatcgagactccgaaaatatg
|
19
|
+
ctcgttatccgcctgctttaaagaaaacaactagtggagaagctaagttttataagcactacacaccatgcacttg
|
20
|
+
caagtcaaaatgtggacagcaatgcccttgtttaactcacgaaaattgctgcgagaaatattgcgggtgctcaaag
|
21
|
+
gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctg
|
22
|
+
ctaatcgtgaatgcgatcca gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacacc
|
23
|
+
agtgcaaatccaatgcaagaacatgcaattcctccttcaaaccaataaaaagattctcattggaaagtctgatgtt
|
24
|
+
catggatggggtgcatttacatgggactctct taaaaagaatgagtatctcggagaatatactggagaactgatca
|
25
|
+
ctcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
|
26
|
+
gctcgaaatcgatgctcgccgtaaaggaaacgagttcaaatttctcaatcactcagcaagacctaactgctacgcc
|
27
|
+
aagttgatgattgtgagaggagatcagaggattggtctatttgcggagagagcaatcgaagaaggtgaggagcttt
|
28
|
+
tcttcgactactgctatggaccagaacatgcggattggtcgcgtggtcgagaacctagaaagactggtgcttctaa
|
29
|
+
aaggtctaaggaagcccgtccagctcgttagtttttgatctgaggagaagcagcaattcaagcagtccttttttta
|
30
|
+
tgttatggtatatcaattaataatgtaatgctattttgtgttactaaaccaaaacttaagtttctgttttatttgt
|
31
|
+
tttagggtgttttgtttgtatcatatgtgtcttaactttcaaagttttctttttgtatttcaatttaaaaacaatg
|
32
|
+
tttatgttgtt
|
33
|
+
|
34
|
+
>At1g65300: mRNA 837bp
|
35
|
+
atgaagagaaagatgaagttatcgttaatagaaaacagtgtatcgaggaaaacaacattcaccaaaaggaagaaag
|
36
|
+
ggatgacgaagaaactaaccgagctagtcactctatgtggtgttgaagcatgtgcggtcgtctatagtccgttcaa
|
37
|
+
ctcgatcccggaggcttggccgtcaagggaaggcgttgaagacgtggtgtcgaaatttatggagttgtcggtgttg
|
38
|
+
gaccggaccaagaagatggtggatcaagagacttttataagtcaaaggatcgccaaagaaaaagagcagctgcaga
|
39
|
+
agctacgtgatgagaaccataattctcagattcgggagttaatgtttggttgtctcaaaggggagacgaatgtgta
|
40
|
+
taatcttgatggaagggatcttcaagatttgagtttatatattgataagtatcttaatggtcttactcgcaggatt
|
41
|
+
ga gatcctTAttgagaacggtgagtcttcttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
|
42
|
+
gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
|
43
|
+
tgatttttatgatcagattccaaagaaaattcatggttt taatatgaatatgaataaggattcgaatcaaagtatg
|
44
|
+
gttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccacc
|
45
|
+
ccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctcta
|
46
|
+
g
|
47
|
+
|
48
|
+
>At1g65300: mRNA 837bp (shortened at end)
|
49
|
+
atgaagagaaagatgaagttatcgttaatagaaaacagtgtatcgaggaaaacaacattcaccaaaaggaagaaag
|
50
|
+
ggatgacgaagaaactaaccgagctagtcactctatgtggtgttgaagcatgtgcggtcgtctatagtccgttcaa
|
51
|
+
ctcgatcccggaggcttggccgtcaagggaaggcgttgaagacgtggtgtcgaaatttatggagttgtcggtgttg
|
52
|
+
gaccggaccaagaagatggtggatcaagagacttttataagtcaaaggatcgccaaagaaaaagagcagctgcaga
|
53
|
+
agctacgtgatgagaaccataattctcagattcgggagttaatgtttggttgtctcaaaggggagacgaatgtgta
|
54
|
+
taatcttgatggaagggatcttcaagatttgagtttatatattgataagtatcttaatggtcttactcgcaggatt
|
55
|
+
gagatcctTAttgagaacggtgagtcttcttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
|
56
|
+
gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
|
57
|
+
tgatttttatgatcag
|
58
|
+
|
59
|
+
|
60
|
+
>At1g65300: mRNA 837bp (shortened from start)
|
61
|
+
ttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
|
62
|
+
gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
|
63
|
+
tgatttttatgatcagattccaaagaaaattcatggttttaatatgaatatgaataaggattcgaatcaaagtatg
|
64
|
+
gttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccacc
|
65
|
+
ccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctcta
|
66
|
+
g
|
67
|
+
|
68
|
+
|
69
|
+
>At1g02580 - shortened for test - inserted cutpoint
|
70
|
+
gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctg
|
71
|
+
ctaatcgtgaatgcgatcca gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacacc
|
72
|
+
agtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggt
|
73
|
+
tttaattggggtgcatttacatgggactctct taaaaagaatgagtatctcggagaatatactggagaactgatca
|
74
|
+
ctcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
|
75
|
+
|
@@ -0,0 +1,21 @@
|
|
1
|
+
>At1g11545.1 68414.m01326 xyloglucan:xyloglucosyl transferase, putative / xyloglucan endotransglycosylase, putative / endo-xyloglucan transferase, putative similar to endo-xyloglucan transferase GI:2244732 from [Gossypium hirsutum]
|
2
|
+
actcacggaacaagtgtagattgcattacctctctctctctctctcttcgaaatattcga
|
3
|
+
agtagagacaaccaATGGAGACGGAAAGGAGGATCATAACGAGCTGTTCTGCCATGACGG
|
4
|
+
CTCTGTTCTTGTTCATGACGGCTCTAATGGCGTCGTCCTCTATCGCAGCAACACCGACAC
|
5
|
+
AATCGTTTGAAGATAATTTCAACATTATGTGGTCTGAAAATCACTTCACGACTTCCGATG
|
6
|
+
ATGGAGAGATCTGGAATCTTTCCTTAGATAACGACACCGGATGTGGATTTCAGACAAAGC
|
7
|
+
ACATGTATAGATTCGGATGGTTTAGTATGAAGCTAAAGCTCGTCGGAGGCGACTCCGCCG
|
8
|
+
GCGTCGTCACCGCTTACTACATGTGTTCGGAGAATGGGGCAGGACCGGAGAGAGACGAGA
|
9
|
+
TAGATTTCGAATTTCTAGGGAACCGAACCGGACAGCCTTACATTATTCAGACCAATGTGT
|
10
|
+
ATAAGAACGGAACCGGGAATCGGGAGATGCGACATTCCCTCTGGTTCGACCCGACCAAGG
|
11
|
+
ATTATCACACCTACTCAATTCTTTGGAATAACCACCAGCTTGTGTTCTTCGTGGATAGGG
|
12
|
+
TACCAATTCGAGTATACAAGAACAGTGATAAGGTACCAAACAACGACTTCTTCCCGAACC
|
13
|
+
AGAAGCCGATGTACTTGTTCTCCAGCATTTGGAACGCTGACGATTGGGCTACACGTGGTG
|
14
|
+
GTCTGGAGAAGACTGACTGGAAAAAAGCTCCATTCGTCTCTTCTTACAAGGACTTCGCCG
|
15
|
+
TCGAAGGCTGCCGTTGGAAGGATCCATTCCCTGCATGCGTCTCTACCACAACAGAGAATT
|
16
|
+
GGTGGGATCAGTACGACGCGTGGCATTTGTCCAAGACACAGAAGATGGATTATGCGTGGG
|
17
|
+
TGCAGCGTAATCTCGTCGTATACGATTATTGCAAAGACAGTGAGAGGTTCCCTACTCTTC
|
18
|
+
CTTGGGAGTGTTCCATTAGCCCTTGGGCTTAAaatcaattttgttttgagtgtattaaag
|
19
|
+
tggaaatggtttatgtaataattttactctcttttttttggcatttcttattttgttatg
|
20
|
+
gactatatcctctgtttatttatttaattaattatttatttagtcggctat
|
21
|
+
|
@@ -0,0 +1,63 @@
|
|
1
|
+
GENSCAN 1.0 Date run: 30-May-103 Time: 14:06:28
|
2
|
+
|
3
|
+
Sequence HUMRASH : 12942 bp : 68.17% C+G : Isochore 4 (57 - 100 C+G%)
|
4
|
+
|
5
|
+
Parameter matrix: HumanIso.smat
|
6
|
+
|
7
|
+
Predicted genes/exons:
|
8
|
+
|
9
|
+
Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
|
10
|
+
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
|
11
|
+
|
12
|
+
1.01 Init + 1664 1774 111 1 0 94 83 212 0.997 21.33
|
13
|
+
1.02 Intr + 2042 2220 179 1 2 104 66 408 0.997 40.12
|
14
|
+
1.03 Intr + 2374 2533 160 1 1 89 94 302 0.999 32.08
|
15
|
+
1.04 Term + 3231 3350 120 2 0 115 48 202 0.980 18.31
|
16
|
+
1.05 PlyA + 3722 3727 6 -5.80
|
17
|
+
|
18
|
+
2.00 Prom + 6469 6508 40 -7.92
|
19
|
+
2.01 Init + 8153 8263 111 1 0 94 83 212 0.998 21.33
|
20
|
+
2.02 Intr + 8531 8709 179 1 2 104 66 408 0.997 40.12
|
21
|
+
2.03 Intr + 8863 9022 160 1 1 89 94 302 0.999 32.08
|
22
|
+
2.04 Term + 9720 9839 120 2 0 115 48 202 0.961 18.31
|
23
|
+
|
24
|
+
Predicted peptide sequence(s):
|
25
|
+
|
26
|
+
Predicted coding sequence(s):
|
27
|
+
|
28
|
+
|
29
|
+
>HUMRASH|GENSCAN_predicted_peptide_1|189_aa
|
30
|
+
MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
|
31
|
+
QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
|
32
|
+
AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
|
33
|
+
CMSCKCVLS
|
34
|
+
|
35
|
+
>HUMRASH|GENSCAN_predicted_CDS_1|570_bp
|
36
|
+
atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
|
37
|
+
atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
|
38
|
+
cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
|
39
|
+
caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
|
40
|
+
gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
|
41
|
+
aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
|
42
|
+
gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
|
43
|
+
tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
|
44
|
+
cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
|
45
|
+
tgcatgagctgcaagtgtgtgctctcctga
|
46
|
+
|
47
|
+
>HUMRASH|GENSCAN_predicted_peptide_2|189_aa
|
48
|
+
MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
|
49
|
+
QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
|
50
|
+
AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
|
51
|
+
CMSCKCVLS
|
52
|
+
|
53
|
+
>HUMRASH|GENSCAN_predicted_CDS_2|570_bp
|
54
|
+
atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
|
55
|
+
atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
|
56
|
+
cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
|
57
|
+
caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
|
58
|
+
gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
|
59
|
+
aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
|
60
|
+
gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
|
61
|
+
tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
|
62
|
+
cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
|
63
|
+
tgcatgagctgcaagtgtgtgctctcctga
|
@@ -0,0 +1,32 @@
|
|
1
|
+
Q9RHD9 D44DAE8C544CB7C1 267 HMMPfam PF00575 S1 1 55 3.3E-6 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
2
|
+
Q9RHD9 D44DAE8C544CB7C1 267 HMMPfam PF00575 S1 68 142 4.1E-19 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
3
|
+
Q9RHD9 D44DAE8C544CB7C1 267 HMMPfam PF00575 S1 155 228 1.8E-19 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
4
|
+
Q9RHD9 D44DAE8C544CB7C1 267 HMMSmart SM00316 S1 3 55 7.1E-7 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
5
|
+
Q9RHD9 D44DAE8C544CB7C1 267 HMMSmart SM00316 S1 70 142 8.1E-20 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
6
|
+
Q9RHD9 D44DAE8C544CB7C1 267 HMMSmart SM00316 S1 157 228 1.5E-21 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
7
|
+
Q9RHD9 D44DAE8C544CB7C1 267 ProfileScan PS50126 S1 1 55 14.869 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
8
|
+
Q9RHD9 D44DAE8C544CB7C1 267 ProfileScan PS50126 S1 72 142 20.809 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
9
|
+
Q9RHD9 D44DAE8C544CB7C1 267 ProfileScan PS50126 S1 159 228 22.541 T 11-Nov-2005 IPR003029 RNA binding S1 Molecular Function:RNA binding (GO:0003723)
|
10
|
+
Q9RHD9 D44DAE8C544CB7C1 267 FPrintScan PR00681 RIBOSOMALS1 6 27 1.5E-17 T 11-Nov-2005 IPR000110 Ribosomal protein S1 Molecular Function:RNA binding (GO:0003723), Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
11
|
+
Q9RHD9 D44DAE8C544CB7C1 267 FPrintScan PR00681 RIBOSOMALS1 85 104 1.5E-17 T 11-Nov-2005 IPR000110 Ribosomal protein S1 Molecular Function:RNA binding (GO:0003723), Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
12
|
+
Q9RHD9 D44DAE8C544CB7C1 267 FPrintScan PR00681 RIBOSOMALS1 125 143 1.5E-17 T 11-Nov-2005 IPR000110 Ribosomal protein S1 Molecular Function:RNA binding (GO:0003723), Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
13
|
+
Q9RHD9 D44DAE8C544CB7C1 267 superfamily SSF50249 Nucleic_acid_OB 3 60 1.4E-7 T 11-Nov-2005 IPR008994 Nucleic acid-binding OB-fold Molecular Function:nucleic acid binding (GO:0003676)
|
14
|
+
Q9RHD9 D44DAE8C544CB7C1 267 superfamily SSF50249 Nucleic_acid_OB 61 205 6.3999999999999995E-24 T 11-Nov-2005 IPR008994 Nucleic acid-binding OB-fold Molecular Function:nucleic acid binding (GO:0003676)
|
15
|
+
RS16_ECOLI F94D07049A6D489D 82 HMMTigr TIGR00002 S16 2 81 117.16 T 11-Nov-2005 IPR000307 Ribosomal protein S16 Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
16
|
+
RS16_ECOLI F94D07049A6D489D 82 superfamily SSF54565 Ribosomal_S16 1 79 1.81E-8 T 11-Nov-2005 IPR000307 Ribosomal protein S16 Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
17
|
+
RS16_ECOLI F94D07049A6D489D 82 HMMPfam PF00886 Ribosomal_S16 8 68 2.7000000000000004E-33 T 11-Nov-2005 IPR000307 Ribosomal protein S16 Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
18
|
+
RS16_ECOLI F94D07049A6D489D 82 BlastProDom PD003791 Ribosomal_S16 10 77 4.0E-33 T 11-Nov-2005 IPR000307 Ribosomal protein S16 Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
19
|
+
RS16_ECOLI F94D07049A6D489D 82 ProfileScan PS00732 RIBOSOMAL_S16 2 11 8.0E-5 T 11-Nov-2005 IPR000307 Ribosomal protein S16 Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
|
20
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 superfamily SSF47384 His_kin_homodim 220 292 5.89E-7 T 11-Nov-2005 IPR009082 Histidine kinase, homodimeric
|
21
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 HMMSmart SM00304 HAMP 170 222 1.8E-6 T 11-Nov-2005 IPR003660 Histidine kinase, HAMP region Molecular Function:signal transducer activity (GO:0004871), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
|
22
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 ProfileScan PS50885 HAMP 170 222 7.777 T 11-Nov-2005 IPR003660 Histidine kinase, HAMP region Molecular Function:signal transducer activity (GO:0004871), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
|
23
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 HMMPfam PF00672 HAMP 151 219 1.1E-8 T 11-Nov-2005 IPR003660 Histidine kinase, HAMP region Molecular Function:signal transducer activity (GO:0004871), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
|
24
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 ProfileScan PS50109 HIS_KIN 237 446 34.449 T 11-Nov-2005 IPR005467 Histidine kinase Biological Process:protein amino acid phosphorylation (GO:0006468), Molecular Function:kinase activity (GO:0016301)
|
25
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 HMMSmart SM00388 HisKA 230 296 1.4E-12 T 11-Nov-2005 IPR003661 Histidine kinase A, N-terminal Molecular Function:two-component sensor molecule activity (GO:0000155), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
|
26
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 HMMPfam PF00512 HisKA 230 296 2.4E-11 T 11-Nov-2005 IPR003661 Histidine kinase A, N-terminal Molecular Function:two-component sensor molecule activity (GO:0000155), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
|
27
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 HMMSmart SM00387 HATPase_c 338 446 2.9E-24 T 11-Nov-2005 IPR003594 ATP-binding region, ATPase-like Molecular Function:ATP binding (GO:0005524)
|
28
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 HMMPfam PF02518 HATPase_c 338 445 2.5E-26 T 11-Nov-2005 IPR003594 ATP-binding region, ATPase-like Molecular Function:ATP binding (GO:0005524)
|
29
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 FPrintScan PR00344 BCTRLSENSOR 374 388 2.0E-12 T 11-Nov-2005 IPR004358 Histidine kinase related protein, C-terminal Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)
|
30
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 FPrintScan PR00344 BCTRLSENSOR 392 402 2.0E-12 T 11-Nov-2005 IPR004358 Histidine kinase related protein, C-terminal Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)
|
31
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 FPrintScan PR00344 BCTRLSENSOR 406 424 2.0E-12 T 11-Nov-2005 IPR004358 Histidine kinase related protein, C-terminal Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)
|
32
|
+
Y902_MYCTU CD84A335CCFFE6D7 446 FPrintScan PR00344 BCTRLSENSOR 430 443 2.0E-12 T 11-Nov-2005 IPR004358 Histidine kinase related protein, C-terminal Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)
|
@@ -0,0 +1,74 @@
|
|
1
|
+
Sequence "Q9RHD9" crc64 checksum: D44DAE8C544CB7C1 length: 267 aa.
|
2
|
+
|
3
|
+
InterPro IPR000110 Ribosomal protein S1
|
4
|
+
Molecular Function: RNA binding (GO:0003723), Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: ribosome (GO:0005840), Biological Process: protein biosynthesis (GO:0006412)
|
5
|
+
method AccNumber shortName location
|
6
|
+
FPrintScan PR00681 RIBOSOMALS1 T[6-27] 1.5e-17 T[85-104] 1.5e-17 T[125-143] 1.5e-17
|
7
|
+
|
8
|
+
InterPro IPR003029 RNA binding S1
|
9
|
+
Molecular Function: RNA binding (GO:0003723)
|
10
|
+
method AccNumber shortName location
|
11
|
+
HMMPfam PF00575 S1 T[1-55] 1.3e-08 T[68-142] 1.6e-21 T[155-228] 6.8e-22
|
12
|
+
HMMSmart SM00316 S1 T[3-55] 1.2e-06 T[70-142] 1.4e-19 T[157-228] 2.6e-21
|
13
|
+
ProfileScan PS50126 S1 T[1-55] 14.869 T[72-142] 20.809 T[159-228] 22.541
|
14
|
+
|
15
|
+
InterPro IPR008994 Nucleic acid-binding OB-fold
|
16
|
+
method AccNumber shortName location
|
17
|
+
superfamily SSF50249 Nucleic acid-binding proteins T[147-257] 2.5e-24 T[59-145] 2.4e-22 T[3-58] 9.2e-14
|
18
|
+
|
19
|
+
InterPro NULL NULL
|
20
|
+
method AccNumber shortName location
|
21
|
+
Coil coil coiled-coil ?[225-246]
|
22
|
+
Seg seg seg ?[29-40] ?[84-98] ?[222-237]
|
23
|
+
|
24
|
+
Sequence "RS16_ECOLI" crc64 checksum: F94D07049A6D489D length: 82 aa.
|
25
|
+
|
26
|
+
InterPro IPR000307 Ribosomal protein S16
|
27
|
+
Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: intracellular (GO:0005622), Cellular Component: ribosome (GO:0005840), Biological Process: protein biosynthesis (GO:0006412)
|
28
|
+
method AccNumber shortName location
|
29
|
+
BlastProDom PD003791 sp_RS16_ECOLI_P02372; T[1-77] 3e-38
|
30
|
+
HMMPfam PF00886 Ribosomal_S16 T[8-68] 1.1e-35
|
31
|
+
HMMTigr TIGR00002 S16 T[2-81] 8.8e-33
|
32
|
+
ScanRegExp PS00732 RIBOSOMAL_S16 T[2-11] 8e-5
|
33
|
+
superfamily SSF54565 Ribosomal protein S16 T[1-79] 9.4e-28
|
34
|
+
|
35
|
+
Sequence "Y902_MYCTU" crc64 checksum: CD84A335CCFFE6D7 length: 446 aa.
|
36
|
+
|
37
|
+
InterPro IPR003594 ATP-binding region, ATPase-like
|
38
|
+
Molecular Function: ATP binding (GO:0005524)
|
39
|
+
method AccNumber shortName location
|
40
|
+
HMMPfam PF02518 HATPase_c T[338-445] 9.6e-29
|
41
|
+
HMMSmart SM00387 HATPase_c T[338-446] 5e-24
|
42
|
+
|
43
|
+
InterPro IPR003660 Histidine kinase, HAMP region
|
44
|
+
Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
|
45
|
+
method AccNumber shortName location
|
46
|
+
HMMPfam PF00672 HAMP T[151-219] 4.3e-11
|
47
|
+
HMMSmart SM00304 HAMP T[170-222] 3.1e-06
|
48
|
+
ProfileScan PS50885 HAMP T[170-222] 7.777
|
49
|
+
|
50
|
+
InterPro IPR003661 Histidine kinase A, N-terminal
|
51
|
+
Molecular Function: two-component sensor molecule activity (GO:0000155), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
|
52
|
+
method AccNumber shortName location
|
53
|
+
HMMPfam PF00512 HisKA T[230-296] 9.2e-14
|
54
|
+
HMMSmart SM00388 HisKA T[230-296] 2.4e-12
|
55
|
+
|
56
|
+
InterPro IPR004358 Bacterial sensor protein, C-terminal
|
57
|
+
Molecular Function: two-component sensor molecule activity (GO:0000155), Biological Process: signal transduction (GO:0007165)
|
58
|
+
method AccNumber shortName location
|
59
|
+
FPrintScan PR00344 BCTRLSENSOR T[374-388] 2e-12 T[392-402] 2e-12 T[406-424] 2e-12 T[430-443] 2e-12
|
60
|
+
|
61
|
+
InterPro IPR005467 Histidine kinase
|
62
|
+
Biological Process: signal transduction (GO:0007165), Molecular Function: kinase activity (GO:0016301)
|
63
|
+
method AccNumber shortName location
|
64
|
+
ProfileScan PS50109 HIS_KIN T[237-446] 34.449
|
65
|
+
|
66
|
+
InterPro IPR009082 Histidine kinase, homodimeric
|
67
|
+
method AccNumber shortName location
|
68
|
+
superfamily SSF47384 Homodimeric domain of signal transducing histidine kinase T[220-292] 2.7e-11
|
69
|
+
|
70
|
+
InterPro NULL NULL
|
71
|
+
method AccNumber shortName location
|
72
|
+
Seg seg seg ?[44-55] ?[108-120] ?[160-173] ?[308-319] ?[400-424]
|
73
|
+
superfamily SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase T[295-444] 4.6e-30
|
74
|
+
|
@@ -0,0 +1,30 @@
|
|
1
|
+
seqfile = abglobin.aa
|
2
|
+
treefile = abglobin.trees
|
3
|
+
outfile = output.txt
|
4
|
+
clock = 0
|
5
|
+
ncatG = 8
|
6
|
+
noisy = 0
|
7
|
+
fix_omega = 0
|
8
|
+
aaDist = 0
|
9
|
+
fix_kappa = 1
|
10
|
+
getSE = 0
|
11
|
+
runmode = 0
|
12
|
+
omega = 0.4
|
13
|
+
aaRatefile = wag.dat
|
14
|
+
method = 0
|
15
|
+
seqtype = 2
|
16
|
+
NSsites = 0
|
17
|
+
fix_alpha = 0
|
18
|
+
RateAncestor = 1
|
19
|
+
verbose = 1
|
20
|
+
icode = 0
|
21
|
+
model = 1
|
22
|
+
alpha = 0.5
|
23
|
+
Small_Diff = 5.0e-06
|
24
|
+
CodonFreq = 2
|
25
|
+
cleandata = 1
|
26
|
+
ndata = 1
|
27
|
+
Mgene = 0
|
28
|
+
kappa = 2
|
29
|
+
Malpha = 0
|
30
|
+
fix_blength = 0
|
@@ -0,0 +1,78 @@
|
|
1
|
+
|
2
|
+
seed used = 552599837
|
3
|
+
|
4
|
+
|
5
|
+
Data set 1
|
6
|
+
5 285
|
7
|
+
|
8
|
+
human VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY RLTPEEKSAV TALWGKVNVD EVGGEALGRL LVVYPWTQRF FESFGDLSTP DAVMGNPKVK AHGKKVLGAF SDGLAHLDNL KGTFATLSEL HCDKLHVDPE NFRLLGNVLV CVLAHHFGKE FTPPVQAAYQ KVVAGVANAL AHKYH
|
9
|
+
goat-cow VLSAADKSNV KAAWGKVGGN AGAYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGE KVAAALTKAV GHLDDLPGTL SDLSDLHAHK LRVDPVNFKL LSHSLLVTLA CHLPNDFTPA VHASLDKFLA NVSTVLTSKY RLTAEEKAAV TAFWGKVKVD EVGGEALGRL LVVYPWTQRF FESFGDLSTA DAVMNNPKVK AHGKKVLDSF SNGMKHLDDL KGTFAALSEL HCDKLHVDPE NFKLLGNVLV VVLARNFGKE FTPVLQADFQ KVVAGVANAL AHRYH
|
10
|
+
rabbit VLSPADKTNI KTAWEKIGSH GGEYGAEAVE RMFLGFPTTK TYFPHFDFTH GSEQIKAHGK KVSEALTKAV GHLDDLPGAL STLSDLHAHK LRVDPVNFKL LSHCLLVTLA NHHPSEFTPA VHASLDKFLA NVSTVLTSKY RLSSEEKSAV TALWGKVNVE EVGGEALGRL LVVYPWTQRF FESFGDLSSA NAVMNNPKVK AHGKKVLAAF SEGLSHLDNL KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV IVLSHHFGKE FTPQVQAAYQ KVVAGVANAL AHKYH
|
11
|
+
rat VLSADDKTNI KNCWGKIGGH GGEYGEEALQ RMFAAFPTTK TYFSHIDVSP GSAQVKAHGK KVADALAKAA DHVEDLPGAL STLSDLHAHK LRVDPVNFKF LSHCLLVTLA CHHPGDFTPA MHASLDKFLA SVSTVLTSKY RLTDAEKAAV NALWGKVNPD DVGGEALGRL LVVYPWTQRY FDSFGDLSSA SAIMGNPKVK AHGKKVINAF NDGLKHLDNL KGTFAHLSEL HCDKLHVDPE NFRLLGNMIV IVLGHHLGKE FTPCAQAAFQ KVVAGVASAL AHKYH
|
12
|
+
marsupial VLSDADKTHV KAIWGKVGGH AGAYAAEALA RTFLSFPTTK TYFPHFDLSP GSAQIQGHGK KVADALSQAV AHLDDLPGTM SKLSDLHAHK LRVDPVNFKL LSHCLIVTLA AHLSKDLTPE VHASMDKFFA SVATVLTSKY RLTSEEKNCI TTIWSKVQVD QTGGEALGRM LVVYPWTTRF FGSFGDLSSP GAVMSNSKVQ AHGAKVLTSF GEAVKHLDNL KGTYAKLSEL HCDKLHVDPE NFKMLGNIIV ICLAEHFGKD FTPECQVAWQ KLVAGVAHAL AHKYH
|
13
|
+
|
14
|
+
|
15
|
+
|
16
|
+
Printing out site pattern counts
|
17
|
+
|
18
|
+
|
19
|
+
5 126 P
|
20
|
+
|
21
|
+
human VLSPADKTNV AAWGGAHAEY GAEALERMFL SPTPHFLSHA QVKGKADTNV AVDMNALANL CLALPAEFAV LSSTPESAVT ALGNVDEVQF ETPDVMGKLG ASDLANFTCR VLCVAHFEPV AAYVNK
|
22
|
+
goat-cow VLSAADKSNV AAWGGGNAAY GAEALERMFL SPTPHFLSHA QVKGEAATKV GLDLGTLDNL SLCLPNDFAV LNSTAEAAVT AFGKVDEVQF ETADVMNKLD SSNMKDFACK VLVVARFEVL ADFVNR
|
23
|
+
rabbit VLSPADKTNI TAWEGSHGEY GAEAVERMFL GPTPHFFTHE QIKAKSETKV GLDLGALTNL CLNHPSEFAV LNSSSESAVT ALGNVEEVQF ESANVMNKLA ASELSNFKCR VLIVSHFEQV AAYVNK
|
24
|
+
rat VLSADDKTNI NCWGGGHGEY GEEALQRMFA APTSHIVSPA QVKAKADAKA DVELGALTNF CLCHPGDFAM LSSTDAAAVN ALGNPDDVQY DSASIMGKIN ANDLKNFHCR MIIVGHLECA AAFVSK
|
25
|
+
marsupial VLSDADKTHV AIWGGGHAAY AAEALARTFL SPTPHFLSPA QIQGKADSQV ALDLGTMKNL CIALSKDLEV FSATSENCIT TISQVDQTTF GSPGVMSALT SGEVKNYKCK IIICAEFDEC VAWLHK
|
26
|
+
|
27
|
+
|
28
|
+
|
29
|
+
16 21 10 1 1 10 17 1 1 2 1 1 3 1 13
|
30
|
+
1 2 1 1 5 2 1 5 15 1 1 5 1 10 1
|
31
|
+
1 7 10 1 14 1 1 1 1 1 3 1 2 1 1
|
32
|
+
1 1 1 1 1 1 1 1 1 1 1 4 1 4 1
|
33
|
+
1 1 1 1 2 1 1 1 1 1 1 1 1 1 1
|
34
|
+
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
|
35
|
+
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
|
36
|
+
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
|
37
|
+
1 1 1 1 1 1
|
38
|
+
|
39
|
+
AAML (in paml version 4, June 2007) ./test/material/codeml/abglobin.aa Model: EqualInput dGamma (ncatG=8) ns = 5 ls = 285
|
40
|
+
|
41
|
+
|
42
|
+
Frequencies..
|
43
|
+
A R N D C Q E G H I L K M F P S T W Y V
|
44
|
+
human 0.1263 0.0211 0.0351 0.0526 0.0105 0.0140 0.0421 0.0702 0.0632 0.0000 0.1263 0.0772 0.0105 0.0526 0.0491 0.0561 0.0561 0.0105 0.0211 0.1053
|
45
|
+
goat-cow 0.1193 0.0246 0.0421 0.0632 0.0070 0.0140 0.0386 0.0737 0.0526 0.0000 0.1298 0.0842 0.0105 0.0596 0.0351 0.0596 0.0526 0.0105 0.0175 0.1053
|
46
|
+
rabbit 0.0982 0.0211 0.0421 0.0386 0.0070 0.0175 0.0596 0.0702 0.0667 0.0140 0.1228 0.0842 0.0070 0.0561 0.0386 0.0737 0.0561 0.0105 0.0211 0.0947
|
47
|
+
rat 0.1193 0.0211 0.0386 0.0667 0.0175 0.0175 0.0316 0.0807 0.0667 0.0246 0.1123 0.0842 0.0140 0.0491 0.0386 0.0596 0.0456 0.0105 0.0211 0.0807
|
48
|
+
marsupial 0.1088 0.0175 0.0211 0.0561 0.0175 0.0281 0.0351 0.0702 0.0632 0.0281 0.1088 0.0842 0.0175 0.0491 0.0351 0.0737 0.0667 0.0140 0.0211 0.0842
|
49
|
+
|
50
|
+
Homogeneity statistic: X2 = 0.13569 G = 0.15654
|
51
|
+
|
52
|
+
Average 0.114386 0.021053 0.035789 0.055439 0.011930 0.018246 0.041404 0.072982 0.062456 0.013333 0.120000 0.082807 0.011930 0.053333 0.039298 0.064561 0.055439 0.011228 0.020351 0.094035
|
53
|
+
|
54
|
+
# constant sites: 170 (59.65%)
|
55
|
+
ln Lmax (unconstrained) = -1189.106658
|
56
|
+
|
57
|
+
|
58
|
+
TREE # 1: (((3, 4), 1), 2, 5); MP score: 177
|
59
|
+
lnL(ntime: 7 np: 8): -1817.465211 +0.000000
|
60
|
+
6..7 7..8 8..3 8..4 7..1 6..2 6..5
|
61
|
+
0.033639 0.038008 0.082889 0.187866 0.055050 0.096992 0.284574 0.588710
|
62
|
+
|
63
|
+
tree length = 0.77902
|
64
|
+
|
65
|
+
(((3: 0.082889, 4: 0.187866): 0.038008, 1: 0.055050): 0.033639, 2: 0.096992, 5: 0.284574);
|
66
|
+
|
67
|
+
(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);
|
68
|
+
|
69
|
+
Detailed output identifying parameters
|
70
|
+
|
71
|
+
alpha (gamma, K = 8) = 0.58871
|
72
|
+
rate: 0.01357 0.09006 0.22445 0.42476 0.71414 1.14510 1.85916 3.52875
|
73
|
+
freq: 0.12500 0.12500 0.12500 0.12500 0.12500 0.12500 0.12500 0.12500
|
74
|
+
|
75
|
+
Time used: 0:01
|
76
|
+
|
77
|
+
|
78
|
+
Data set 2
|
@@ -0,0 +1,217 @@
|
|
1
|
+
|
2
|
+
Estimated rates for sites from AAML.
|
3
|
+
(((FYDL177C: 0.089767, PYDL177C: 0.044687): 0.021205, MYDL177C: 0.096521): 0.108719, BYDL177C: 0.058006);
|
4
|
+
|
5
|
+
Frequencies and rates for categories (K=8)
|
6
|
+
rate: 0.03346 0.14763 0.30690 0.51693 0.79689 1.18983 1.81043 3.19794
|
7
|
+
freq: 0.12500 0.12500 0.12500 0.12500 0.12500 0.12500 0.12500 0.12500
|
8
|
+
|
9
|
+
Site Freq Data Rate (posterior mean & category)
|
10
|
+
|
11
|
+
1 1 ***M 1.000 5
|
12
|
+
2 2 ***H 1.000 1
|
13
|
+
3 2 ***H 1.000 1
|
14
|
+
4 4 ***L 1.000 7
|
15
|
+
5 2 ***S 1.000 1
|
16
|
+
6 1 ***P 1.000 7
|
17
|
+
7 1 ***I 1.000 6
|
18
|
+
8 3 ***K 1.000 1
|
19
|
+
9 3 ***K 1.000 1
|
20
|
+
10 2 ***T 1.000 8
|
21
|
+
11 4 ***L 1.000 7
|
22
|
+
12 1 ***Y 1.000 8
|
23
|
+
13 3 ***K 1.000 1
|
24
|
+
14 1 ***A 1.000 7
|
25
|
+
15 4 ***L 1.000 7
|
26
|
+
16 1 ***D 1.000 2
|
27
|
+
17 1 ***R 1.000 8
|
28
|
+
18 1 ***N 1.000 1
|
29
|
+
19 1 ***Q 1.000 7
|
30
|
+
20 2 ***C 1.000 3
|
31
|
+
21 4 ***L 1.000 7
|
32
|
+
22 2 ***T 1.000 8
|
33
|
+
23 2 ***S 1.000 1
|
34
|
+
24 1 ***V 1.000 8
|
35
|
+
25 1 ***F 1.000 8
|
36
|
+
26 2 ***C 1.000 3
|
37
|
+
27 2 ***E 1.000 8
|
38
|
+
28 2 ***E 1.000 8
|
39
|
+
29 3 MMMM 0.638 1
|
40
|
+
30 1 SSSN 1.473 7
|
41
|
+
31 15 KKKK 0.645 1
|
42
|
+
32 6 NNNN 0.624 1
|
43
|
+
33 7 VVVV 0.709 1
|
44
|
+
34 8 GGGG 0.828 1
|
45
|
+
35 1 KRKK 1.510 7
|
46
|
+
36 13 LLLL 0.779 1
|
47
|
+
37 7 VVVV 0.709 1
|
48
|
+
38 1 KKKR 1.534 8
|
49
|
+
39 3 VIII 1.539 8
|
50
|
+
40 3 WWWW 0.861 1
|
51
|
+
41 6 NNNN 0.624 1
|
52
|
+
42 7 EEEE 0.654 1
|
53
|
+
43 7 SSSS 0.629 1
|
54
|
+
44 7 EEEE 0.654 1
|
55
|
+
45 7 VVVV 0.709 1
|
56
|
+
46 13 LLLL 0.779 1
|
57
|
+
47 2 VIVI 2.233 8
|
58
|
+
48 3 DDDD 0.662 1
|
59
|
+
49 8 RRRR 0.651 1
|
60
|
+
50 15 KKKK 0.645 1
|
61
|
+
51 7 SSSS 0.629 1
|
62
|
+
52 15 KKKK 0.645 1
|
63
|
+
53 3 FFFF 0.813 1
|
64
|
+
54 9 QQQQ 0.598 1
|
65
|
+
55 9 AAAA 0.681 1
|
66
|
+
56 8 RRRR 0.651 1
|
67
|
+
57 4 CCCC 0.845 1
|
68
|
+
58 4 CCCC 0.845 1
|
69
|
+
59 1 TTPT 1.553 8
|
70
|
+
60 13 LLLL 0.779 1
|
71
|
+
61 1 RQQQ 1.470 7
|
72
|
+
62 1 NDNN 1.472 7
|
73
|
+
63 9 QQQQ 0.598 1
|
74
|
+
64 15 KKKK 0.645 1
|
75
|
+
65 3 DDDD 0.662 1
|
76
|
+
66 4 IIII 0.671 1
|
77
|
+
67 1 SPPP 1.716 8
|
78
|
+
68 1 SFSF 2.387 8
|
79
|
+
69 3 VIII 1.539 8
|
80
|
+
70 13 LLLL 0.779 1
|
81
|
+
71 1 EQQQ 1.426 7
|
82
|
+
72 1 EDEE 1.509 7
|
83
|
+
73 13 LLLL 0.779 1
|
84
|
+
74 1 VVTT 1.653 8
|
85
|
+
75 9 QQQQ 0.598 1
|
86
|
+
76 2 SNNN 1.463 7
|
87
|
+
77 6 NNNN 0.624 1
|
88
|
+
78 15 KKKK 0.645 1
|
89
|
+
79 1 SASS 1.481 7
|
90
|
+
80 7 VVVV 0.709 1
|
91
|
+
81 7 SSSS 0.629 1
|
92
|
+
82 15 KKKK 0.645 1
|
93
|
+
83 9 AAAA 0.681 1
|
94
|
+
84 7 SSSS 0.629 1
|
95
|
+
85 4 HHHH 0.664 1
|
96
|
+
86 3 MMMM 0.638 1
|
97
|
+
87 4 HHHH 0.664 1
|
98
|
+
88 3 MMMM 0.638 1
|
99
|
+
89 2 YYYY 0.769 1
|
100
|
+
90 9 AAAA 0.681 1
|
101
|
+
91 3 WWWW 0.861 1
|
102
|
+
92 8 RRRR 0.651 1
|
103
|
+
93 5 TTTT 0.647 1
|
104
|
+
94 9 AAAA 0.681 1
|
105
|
+
95 7 EEEE 0.654 1
|
106
|
+
96 2 VIVI 2.233 8
|
107
|
+
97 1 PASS 2.257 8
|
108
|
+
98 2 SNNN 1.463 7
|
109
|
+
99 1 DEND 2.198 8
|
110
|
+
100 1 SLLL 1.779 8
|
111
|
+
101 1 NNHN 1.462 7
|
112
|
+
102 1 SFLF 2.403 8
|
113
|
+
103 9 QQQQ 0.598 1
|
114
|
+
104 1 H*** 1.000 1
|
115
|
+
105 1 G*** 1.000 1
|
116
|
+
106 2 N*** 1.000 1
|
117
|
+
107 9 QQQQ 0.598 1
|
118
|
+
108 1 DDEE 1.646 8
|
119
|
+
109 9 QQQQ 0.598 1
|
120
|
+
110 15 KKKK 0.645 1
|
121
|
+
111 15 KKKK 0.645 1
|
122
|
+
112 15 KKKK 0.645 1
|
123
|
+
113 1 NSGS 2.221 8
|
124
|
+
114 1 GSNS 2.262 8
|
125
|
+
115 15 KKKK 0.645 1
|
126
|
+
116 1 NNAT 2.357 8
|
127
|
+
117 1 HNNN 1.475 7
|
128
|
+
118 15 KKKK 0.645 1
|
129
|
+
119 1 NKSS 2.237 8
|
130
|
+
120 2 NSNN 1.464 7
|
131
|
+
121 2 NSNN 1.464 7
|
132
|
+
122 1 NNSR 2.289 8
|
133
|
+
123 2 N*** 1.000 1
|
134
|
+
124 4 HHHH 0.664 1
|
135
|
+
125 1 GAVA 2.305 8
|
136
|
+
126 1 NNND 1.485 7
|
137
|
+
127 15 KKKK 0.645 1
|
138
|
+
128 1 TSSS 1.476 7
|
139
|
+
129 1 TKRK 2.270 8
|
140
|
+
130 1 KMNK 2.247 8
|
141
|
+
131 1 IVIV 2.243 8
|
142
|
+
132 1 TITT 1.519 7
|
143
|
+
133 1 VVVM 1.621 8
|
144
|
+
134 9 QQQQ 0.598 1
|
145
|
+
135 2 PPPP 0.802 1
|
146
|
+
136 15 KKKK 0.645 1
|
147
|
+
137 6 NNNN 0.624 1
|
148
|
+
138 3 VIII 1.539 8
|
149
|
+
139 7 EEEE 0.654 1
|
150
|
+
140 9 QQQQ 0.598 1
|
151
|
+
141 8 GGGG 0.828 1
|
152
|
+
142 1 CSCC 1.771 8
|
153
|
+
143 9 AAAA 0.681 1
|
154
|
+
144 3 DDDD 0.662 1
|
155
|
+
145 4 CCCC 0.845 1
|
156
|
+
146 8 GGGG 0.828 1
|
157
|
+
147 7 EEEE 0.654 1
|
158
|
+
148 9 AAAA 0.681 1
|
159
|
+
149 1 AGGG 1.762 8
|
160
|
+
150 9 AAAA 0.681 1
|
161
|
+
151 8 GGGG 0.828 1
|
162
|
+
152 9 QQQQ 0.598 1
|
163
|
+
153 8 RRRR 0.651 1
|
164
|
+
154 13 LLLL 0.779 1
|
165
|
+
155 13 LLLL 0.779 1
|
166
|
+
156 5 TTTT 0.647 1
|
167
|
+
157 13 LLLL 0.779 1
|
168
|
+
158 13 LLLL 0.779 1
|
169
|
+
159 7 EEEE 0.654 1
|
170
|
+
160 8 RRRR 0.651 1
|
171
|
+
161 9 AAAA 0.681 1
|
172
|
+
162 6 NNNN 0.624 1
|
173
|
+
163 4 IIII 0.671 1
|
174
|
+
164 3 FFFF 0.813 1
|
175
|
+
165 6 NNNN 0.624 1
|
176
|
+
166 1 IVVV 1.581 8
|
177
|
+
167 13 LLLL 0.779 1
|
178
|
+
168 7 VVVV 0.709 1
|
179
|
+
169 4 IIII 0.671 1
|
180
|
+
170 7 VVVV 0.709 1
|
181
|
+
171 5 TTTT 0.647 1
|
182
|
+
172 8 RRRR 0.651 1
|
183
|
+
173 3 WWWW 0.861 1
|
184
|
+
174 2 YYYY 0.769 1
|
185
|
+
175 8 GGGG 0.828 1
|
186
|
+
176 8 GGGG 0.828 1
|
187
|
+
177 5 TTTT 0.647 1
|
188
|
+
178 2 PPPP 0.802 1
|
189
|
+
179 13 LLLL 0.779 1
|
190
|
+
180 8 GGGG 0.828 1
|
191
|
+
181 7 SSSS 0.629 1
|
192
|
+
182 7 SSSS 0.629 1
|
193
|
+
183 8 RRRR 0.651 1
|
194
|
+
184 3 FFFF 0.813 1
|
195
|
+
185 8 RRRR 0.651 1
|
196
|
+
186 4 HHHH 0.664 1
|
197
|
+
187 4 IIII 0.671 1
|
198
|
+
188 7 SSSS 0.629 1
|
199
|
+
189 5 TTTT 0.647 1
|
200
|
+
190 4 CCCC 0.845 1
|
201
|
+
191 9 AAAA 0.681 1
|
202
|
+
192 7 VVVV 0.709 1
|
203
|
+
193 7 EEEE 0.654 1
|
204
|
+
194 1 STTT 1.494 7
|
205
|
+
195 13 LLLL 0.779 1
|
206
|
+
196 15 KKKK 0.645 1
|
207
|
+
197 15 KKKK 0.645 1
|
208
|
+
198 8 GGGG 0.828 1
|
209
|
+
199 1 GGGE 1.784 8
|
210
|
+
200 1 FYFF 1.749 8
|
211
|
+
201 13 LLLL 0.779 1
|
212
|
+
202 1 PHPP 1.752 8
|
213
|
+
|
214
|
+
lnL = -907.674000
|
215
|
+
|
216
|
+
mean(r^)= 1.0031 var(r^)= 0.2349
|
217
|
+
Accuracy of rate prediction: corr(r^,r) = 0.4236
|