{"id":872,"date":"2022-09-24T19:06:58","date_gmt":"2022-09-24T11:06:58","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=872"},"modified":"2022-09-24T21:12:45","modified_gmt":"2022-09-24T13:12:45","slug":"swiss-prot%e6%b3%a8%e9%87%8a%e8%84%8a%e6%a4%8e%e5%8a%a8%e7%89%a9%e5%9f%ba%e5%9b%a0%e7%bb%84","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=872","title":{"rendered":"Swiss-Prot\u6ce8\u91ca\u810a\u690e\u52a8\u7269\u57fa\u56e0\u7ec4"},"content":{"rendered":"<pre>wget -c ftp:\/\/ftp.uniprot.org\/pub\/databases\/uniprot\/current_release\/knowledgebase\/taxonomic_divisions\/uniprot_sprot_vertebrates.dat.gz\nwget -c ftp:\/\/ftp.uniprot.org\/pub\/databases\/uniprot\/current_release\/knowledgebase\/taxonomic_divisions\/uniprot_trembl_vertebrates.dat.gz\nzcat uniprot_sprot_vertebrates.dat.gz uniprot_trembl_vertebrates.dat.gz &gt; uniprot_vertebrates.dat\nawk '{if (\/^ \/) {gsub(\/ \/, \"\"); print} else if (\/^AC\/) print \"&gt;\" $2}' uniprot_vertebrates.dat &gt; uniprot_vertebrates.fasta\ndiamond makedb --in uniprot_vertebrates.fasta -d uniprot_vertebrates\ndiamond blastp -d uniprot_vertebrates.dmnd -q grass_carp.pep.fasta --evalue 1e-5 &gt; blastp.outfmt6\npython -m jcvi.formats.blast best -n 1 blastp.outfmt6\npython add_annotation_from_dat.py blastp.outfmt6.best \/data\/database\/UniProt-Plant\/uniprot_plants.dat\n<\/pre>\n<p>github\u83b7\u53d6<a href=\"https:\/\/github.com\/xuzhougeng\/myscripts\/tree\/master\/annotation\">add_annotation_from_dat.py<\/a><br \/>\n\u4e4b\u540e\u4f1a\u8f93\u51faswiss_annotation.tsv\uff0c \u8f93\u51fa\u4fe1\u606f\u5305\u62ec\u5982\u4e0b\u51e0\u5217<\/p>\n<p>gene id<br \/>\nuniprot accession<br \/>\nidentity<br \/>\nhomology species<br \/>\nEnsemblPlants<br \/>\nGO ID<br \/>\nGO component, CC\/MF\/BP<br \/>\nevidence<\/p>\n","protected":false},"excerpt":{"rendered":"<p>wget -c ftp:\/\/ftp.uniprot.org\/pub\/databases\/uniprot\/current_release\/knowledgebase\/taxonomic_divisions\/uniprot_sprot_vertebrates.dat.gz wget -c ftp:\/\/ftp.uniprot.org\/pub\/databases\/uniprot\/current_release\/knowledgebase\/taxonomic_divisions\/uniprot_trembl_vertebrates.dat.gz zcat uniprot_sprot_vertebrates.dat.gz uniprot_trembl_vertebrates.dat.gz &gt; uniprot_vertebrates.dat awk &#8216;{if (\/^ \/) {gsub(\/ \/, &#8220;&#8221;); print} else if (\/^AC\/) print &#8220;&gt;&#8221; $2}&#8217; uniprot_vertebrates.dat &gt; uniprot_vertebrates.fasta diamond makedb &#8211;in uniprot_vertebrates.fasta -d uniprot_vertebrates diamond blastp -d uniprot_vertebrates.dmnd -q grass_carp.pep.fasta &#8211;evalue 1e-5 &gt; blastp.outfmt6 python -m jcvi.formats.blast best -n 1 blastp.outfmt6 python add_annotation_from_dat.py blastp.outfmt6.best \/data\/database\/UniProt-Plant\/uniprot_plants.dat [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/872"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=872"}],"version-history":[{"count":5,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/872\/revisions"}],"predecessor-version":[{"id":877,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/872\/revisions\/877"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=872"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=872"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=872"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}