{"id":469,"date":"2019-11-05T17:46:31","date_gmt":"2019-11-05T09:46:31","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=469"},"modified":"2019-11-05T17:46:31","modified_gmt":"2019-11-05T09:46:31","slug":"mlst%e7%bb%86%e8%8f%8c%e5%88%86%e5%9e%8b","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=469","title":{"rendered":"MLST\u7ec6\u83cc\u5206\u578b"},"content":{"rendered":"<p>\u591a\u4f4d\u70b9\u5e8f\u5217\u5206\u578b\uff08multilocus sequence typing,MLST\uff09\u662f\u4e00\u79cd\u57fa\u4e8e\u6838\u9178\u5e8f\u5217\u6d4b\u5b9a\u7684\u7ec6\u83cc\u5206\u578b\u65b9\u6cd5\u3002\u8fd9\u79cd\u65b9\u6cd5\u901a\u8fc7PCR\u6269\u589e\u591a\u4e2a\u7ba1\u5bb6\u57fa\u56e0\u5185\u90e8\u7247\u6bb5\u5e76\u6d4b\u5b9a\u5176\u5e8f\u5217\uff0c\u5206\u6790\u83cc\u682a\u7684\u53d8\u5f02\u3002<\/p>\n<p>\u4f9d\u8d56conda\u5b89\u88c5<\/p>\n<pre>conda install -c conda-forge -c bioconda -c defaults mlst\r\nmlst contigs.fa\r\ncontigs.fa  neisseria  11149  abcZ(672) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6)\r\n\r\nmlst genomes\/*\r\ngenomes\/6008.fna        saureus         239  arcc(2)   aroe(3)   glpf(1)   gmk_(1)   pta_(4)   tpi_(4)   yqil(3)\r\ngenomes\/strep.fasta.gz  ssuis             1  aroA(1)   cpn60(1)  dpr(1)    gki(1)    mutS(1)   recA(1)   thrA(1)\r\ngenomes\/NC_002973.gbk   lmonocytogenes    1  abcZ(3)   bglA(1)   cat(1)    dapE(1)   dat(3)    ldh(1)    lhkA(3)\r\ngenomes\/L550.gbk.bz2    leptospira      152  glmU(26)  pntA(30)  sucA(28)  tpiA(35)  pfkB(39)  mreA(29)  caiB(29)\r\n\r\nmlst --scheme neisseria NM*\r\nNM003.fa   neisseria  4821  abcZ(222)  adk(3)  aroE(58)  fumC(275)  gdh(30)  pdhC(5)  pgm(255)\r\nNM005.gbk  neisseria  177   abcZ(7)    adk(8)  aroE(10)  fumC(38)   gdh(10)  pdhC(1)  pgm(20)\r\nNM011.fa   neisseria  11    abcZ(2)    adk(3)  aroE(4)   fumC(3)    gdh(8)   pdhC(4)  pgm(6)\r\nNMC.gbk.gz neisseria  8     abcZ(2)    adk(3)  aroE(7)   fumC(2)    gdh(8)   pdhC(5)  pgm(2)\r\n\r\nmlst --legacy --scheme neisseria *.fa\r\nFILE      SCHEME     ST    abcZ  adk  aroE  fumC  gdh  pdhC  pgm\r\nNM003.fa  neisseria  11    2     3    4     3       8     4    6\r\nNM009.fa  neisseria  11149 672   3    4     3       8     4    6\r\nMN043.fa  neisseria  11    2     3    4     3       8     4    6\r\nNM051.fa  neisseria  11    2     3    4     3       8     4    6\r\nNM099.fa  neisseria  1287  2     3    4    17       8     4    6\r\nNM110.fa  neisseria  11    2     3    4     3       8     4    6\r\n<\/pre>\n<p>\u94fe\u63a5\uff1a<a href=\"https:\/\/github.com\/tseemann\/mlst\">Mlst\u5b98\u7f51<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u591a\u4f4d\u70b9\u5e8f\u5217\u5206\u578b\uff08multilocus sequence typing,MLST\uff09\u662f\u4e00\u79cd\u57fa\u4e8e\u6838\u9178\u5e8f\u5217\u6d4b\u5b9a\u7684\u7ec6\u83cc\u5206\u578b\u65b9\u6cd5\u3002\u8fd9\u79cd\u65b9\u6cd5\u901a\u8fc7PCR\u6269\u589e\u591a\u4e2a\u7ba1\u5bb6\u57fa\u56e0\u5185\u90e8\u7247\u6bb5\u5e76\u6d4b\u5b9a\u5176\u5e8f\u5217\uff0c\u5206\u6790\u83cc\u682a\u7684\u53d8\u5f02\u3002 \u4f9d\u8d56conda\u5b89\u88c5 conda install -c conda-forge -c bioconda -c defaults mlst mlst contigs.fa contigs.fa neisseria 11149 abcZ(672) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6) mlst genomes\/* genomes\/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3) genomes\/strep.fasta.gz ssuis 1 aroA(1) cpn60(1) dpr(1) gki(1) mutS(1) recA(1) thrA(1) genomes\/NC_002973.gbk lmonocytogenes 1 abcZ(3) bglA(1) cat(1) dapE(1) dat(3) [&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\/469"}],"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=469"}],"version-history":[{"count":1,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/469\/revisions"}],"predecessor-version":[{"id":470,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/469\/revisions\/470"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=469"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=469"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=469"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}