{"id":219,"date":"2022-01-06T18:55:41","date_gmt":"2022-01-06T10:55:41","guid":{"rendered":"https:\/\/linguopeng.top\/?p=219"},"modified":"2022-01-06T18:57:20","modified_gmt":"2022-01-06T10:57:20","slug":"%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e6%af%94%e5%af%b9","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=219","title":{"rendered":"\u540c\u6e90\u57fa\u56e0\u6bd4\u5bf9"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>#\u53ef\u4ee5\u5c06\u6d4b\u5e8f\u57fa\u56e0\u7ec4\u4e0e\u5df2\u77e5\u57fa\u56e0\u96c6\u76f4\u63a5\u8fdb\u884c blast \u6bd4\u5bf9\uff0c\u7136\u540e\u5c06\u6bd4\u5bf9\u4e0a\u7684\u5e8f\u5217\u63d0\u53d6\u51fa\u6765\u4f5c\u4e3a\u57fa\u56e0\u3002\n#\u57fa\u56e0\u7ec4\uff1a NC_009648.1 https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NC_009648.1\/ \n#\u8d28\u7c92\uff1a NC_009649.1 https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NC_009649 \nefetch -db nuccore -format fasta -id NC_009648.1 > MGH78578.fasta \nefetch -db nuccore -format fasta -id NC_009649 >>MGH78578.fasta\n\n#\u4e0b\u8f7d\u53c2\u8003\u5e8f\u5217\u57fa\u56e0\u96c6\n#https:\/\/www.ncbi.nlm.nih.gov\/genome\/?term=NC_009648\nwget -c https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/all\/GCF\/000\/240\/185\/GCF_000240185.1_ASM24018v2\/GCF_000240185.1_ASM24018v2_protein.faa.gz\n#\u5efa\u7acb\u7d22\u5f15\nmakeblastdb -in GCF_000240185.1_ASM24018v2_protein.faa -dbtype prot -parse_seqids -out GCF_000240185.1_ASM24018v2_protein.faa\n#blastx \u6bd4\u5bf9 blastx \n#\u6838\u9178\u5e8f\u5217\u5bf9\u86cb\u767d\u5e93\u7684\u6bd4\u5bf9\uff0c\u5148\u5c06\u6838\u9178\u5e8f\u5217\u7ffb\u8bd1\u6210\u86cb\u767d\u5e8f\u5217\uff08\u6839\u636e\u76f8\u4f4d\u53ef\u4ee5\u7ffb\u8bd1\u4e3a6\u79cd\u53ef\u80fd\u7684\u86cb\u767d\u5e8f\u5217\uff09\uff0c\u7136\u540e\u518d\u4e0e\u86cb\u767d\u5e93\u505a\u6bd4\u5bf9\u3002\nblastx -query MGH78578.fasta -out blast.out -db GCF_000240185.1_ASM24018v2_protein.faa -outfmt 6 -evalue 1e-5\n#\u63d0\u53d6\u6bd4\u5bf9\u533a\u57df\uff0c\u751f\u6210 bed \u6587\u4ef6\nawk '{if ($7 &lt; $8) print $1\"\\t\"$7-1\"\\t\"$8;else print $1\"\\t\"$8-1\"\\t\"$7}' blast.out >gene.bed\n#\u6839\u636e\u6bd4\u5bf9\u4f4d\u70b9\uff0c\u63d0\u53d6\u5e8f\u5217\nseqkit subseq --bed gene.bed MGH78578.fasta >MGH78578_gene.ffn<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-219","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/219","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=219"}],"version-history":[{"count":2,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/219\/revisions"}],"predecessor-version":[{"id":222,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/219\/revisions\/222"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=219"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=219"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=219"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}