{"id":1839,"date":"2013-09-05T17:35:29","date_gmt":"2013-09-05T09:35:29","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1839"},"modified":"2013-09-07T09:40:15","modified_gmt":"2013-09-07T01:40:15","slug":"orthomcl%e4%bb%8b%e7%bb%8d","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1839","title":{"rendered":"OrthoMCL\u4ecb\u7ecd"},"content":{"rendered":"

1. OrthoMCL\u7684\u7528\u9014<\/h1>\n

\u57fa\u4e8e\u5e8f\u5217\u7684\u76f8\u4f3c\u6027\uff0cOrthoMCL\u80fd\u5c06\u4e00\u7ec4proteins\uff08\u6bd4\u5982\u5168\u57fa\u56e0\u7ec4\u7684proteins\uff09\u5f52\u7c7b\u5230ortholog groups\u3001in-paralogs groups\u548cco-orthologs\u3002<\/p>\n

2. OrthoMCL-DB<\/h1>\n

OrthoMCL-DB\u5305\u542b\u4e86\u5f88\u591aproteins\uff0c\u8fd9\u4e9bproteins\u6765\u81ea\u4e00\u4e9b\u5df2\u7ecf\u5b8c\u5168\u6d4b\u5e8f\u7684\u771f\u6838\u6216\u539f\u6838\u751f\u7269\u7684\u57fa\u56e0\u7ec4\u3002OrthoMCL-DB\u5c06\u8fd9\u4e9bproteins\u8fdb\u884c\u4e86\u805a\u7c7b\uff0c\u5206\u6210\u5f88\u591a\u7684ortholog groups\u3002
\n2010.5.31\uff0c\u53d1\u5e03\u4e86OrthoMCL-DB\u7b2c4\u7248\uff0c\u5305\u542b 116,536\u4e2aortholog groups\u30011,270,853\u4e2aproteins\u300188\u4e2a\u771f\u6838\u751f\u7269\u57fa\u56e0\u7ec4\u300116\u4e2a\u53e4\u83cc\u57fa\u56e0\u7ec4\u300134\u4e2a\u7ec6\u83cc\u57fa\u56e0\u7ec4\u3002
\n2011.5.31\uff0c\u53d1\u5e03\u4e86OrthoMCL-DB\u7b2c5\u7248\uff0c\u5305\u542b 124,740\u4e2aortholog groups\u30011,398,546 \u4e2aproteins\u3001150\u4e2a\u57fa\u56e0\u7ec4<\/a>\u3002
\n2013\u5e74\u672b\u5373\u5c06\u53d1\u5e03OrthoMCL-DB\u7b2c6\u7248\u3002<\/p>\n

3. OrthoMCL\u7684\u4e24\u79cd\u4f7f\u7528\u65b9\u6cd5<\/h1>\n

1. OrthoMCL-DB\u7684\u5b98\u7f51\u5df2\u7ecf\u5c06\u6570\u636e\u4e2d\u7684proteins\u8fdb\u884c\u4e86ortholog\u7684\u805a\u7c7b\uff0c\u5176\u7f51\u7ad9\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5de5\u5177\uff0c\u7528\u4e8e\u63a5\u6536\u4e0a\u4f20\u7684\u57fa\u56e0\u7ec4proteins\uff0c\u518d\u5c06\u8fd9\u4e9bproteins group\u5230\u76f8\u5e94\u7684ortholog groups\u4e2d\u3002\u5b98\u7f51\u63d0\u4f9b\u7684\u5de5\u5177Assign your proteins to OrthoMCL Groups<\/a>\u7528\u4e8e\u8fdb\u884c\u5206\u6790\u3002
\n2. \u5982\u679c\u8981\u5bf9\u591a\u4e2a\u57fa\u56e0\u7ec4\u7684proteomes\u8fdb\u884c\u805a\u7c7b\uff0c\u5219\u53ef\u4ee5\u4f7f\u7528OrthoMCL\u5355\u673a\u7248\u7684\u8f6f\u4ef6\u6765\u8fdb\u884c\u8fd0\u7b97\u3002\u5176\u7528\u6cd5\u8be6\u89c1\uff1aOrthoMCL\u7684\u4f7f\u7528<\/a>\u3002<\/p>\n

4. OrthoMCL\u7b97\u6cd5<\/a><\/h1>\n

1. \u5c06\u591a\u4e2aproteomes\u8f6c\u6362\u6210orthomcl\u517c\u5bb9\u7684FASTA\u6587\u4ef6\u3002
\n2. \u79fb\u9664\u4f4e\u8d28\u91cf\u7684\u5e8f\u5217\u3002
\n3. All-versus-All BLASTP with 1e-5 cutoff\u3002\u5373\u4f7f\u7528\u8fd9\u4e9bproteomes\u7684protein sequences\u6784\u5efablast\u6570\u636e\u5e93\uff0c\u518d\u5c06\u6240\u6709\u7684\u8fd9\u4e9b\u5e8f\u5217\u548c\u6570\u636e\u5e93\u8fdb\u884cBLASTP\u6bd4\u5bf9\uff0c\u53d6evalue\u5c0f\u4e8e1e-5\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002
\n4. Filter by percent match length\u3002\u8ba1\u7b97\u6bd4\u5bf9\u7ed3\u679c\u7684percent match length ( \u6240\u6709hsp\u4e2d\u6bd4\u5bf9\u4e0a\u5e8f\u5217\u7684\u957f\u5ea6\u4e4b\u548c \/ \u4e24\u6761\u5e8f\u5217\u4e2d\u77ed\u7684\u90a3\u6761\u5e8f\u5217\u7684\u957f\u5ea6 )\u3002\u53d650%\u7684cutoff\u503c\u3002
\n5. \u5bfb\u627e\u4e0d\u540c\u7269\u79cd\u95f4potential ortholog pairs(\u4e24\u4e24\u7269\u79cd\u7684protein\u5e8f\u5217\u76f8\u4e92\u662fbest hits)\uff1b\u5bfb\u627e\u540c\u4e00\u7269\u79cd\u5185in-paralog pairs\uff08\u76f8\u4e92\u4e4b\u95f4\u662fbetter hits\uff0c\u5373\u5bf9\u4e8e2\u4e2a\u5e8f\u5217\u4e4b\u4e2d\u7684\u4efb\u610f\u4e00\u6761\u5e8f\u5217\uff0c\u548c\u5176in-paralog\u5e8f\u5217\u4e4b\u95f4\u7684evalue\u503c <= \u8fd9\u6761\u5e8f\u5217\u548c\u5176\u5b83\u7269\u79cd\u6bd4\u5bf9\u7684evalue\u503c\uff09.\n6. \u6839\u636e\u4e0a\u4e00\u6b65\u7ed3\u679c\u5bfb\u627eco-ortholog pairs(pairs connected by orhthology and in-paralog,\u5e76\u4e14pairs\u4e4b\u95f4\u7684evalue\u503c\u4f4e\u4e8e1e-5).\n7. \u5bf9\u6240\u6709\u7684pairs\u8fdb\u884cE-values\u7684Normalization\uff0c\u4ee5\u5229\u4e8e\u4e0b\u4e00\u6b65MCL\u7684\u8ba1\u7b97\u3002\u89c1\u4e0b\u4e00\u90e8\u5206\u5185\u5bb9\uff0c\u6216\u53c2\u8003OrthoMCL Algorithm Document<\/a>\u3002
\n8. \u5c06\u6240\u6709\u7684ortholog,in-paralog\u548cco-ortholog pairs\uff0c\u4ee5\u53ca\u5b83\u4eec\u7684\u6807\u51c6\u5316\u540e\u7684weight\u503c\u8f93\u5165\u5230MCL\u7a0b\u5e8f\u4e2d\uff0c\u6765\u8fdb\u884c\u805a\u7c7b\u5206\u7fa4\u3002MCL documentation<\/a><\/p>\n

5. pairs\u7684evalue\u8ba1\u7b97\u548c\u6807\u51c6\u5316<\/h1>\n

pairs\u7684evalue\u8ba1\u7b97\uff1apairs\u7684\u4e24\u6761\u5e8f\u5217\u76f8\u4e92blast\u540e\u6709\u4e24\u4e2aevalue\u503c\uff0c\u8fd9\u4e24\u4e2a\u503c\u5e38\u5e38\u4e0d\u76f8\u7b49\u3002\u4f46\u662f\u4e3a\u4e86\u8ba1\u7b97\u9700\u8981\uff0c\u4e8e\u662fpairs\u7684\u4e4b\u95f4\u7684\u4e24\u4e2aevalue\u503c\u8981\u8fdb\u884c\u4e00\u4e2a\u8ba1\u7b97\uff0c\u5f97\u5230pairs weight\uff0cweight= ( -log10(evalue1) + -log10(evalue2) ) \/ 2 \u3002
\npairs\u7684evalue\u7684\u6807\u51c6\u5316\uff1a1. \u5bf9\u4e8ein-paralog pairs\uff0c\u5728\u67d0\u4e00\u4e2a\u57fa\u56e0\u7ec4\u4e2d\uff0c\u53d6\u4e24\u6761\u5e8f\u5217\u4e2d\u4efb\u610f\u4e00\u6761\u5e8f\u5217\u6709ortholog\u7684in-paralog pairs\u4e3a\u6709\u6548in-paralog pairs\u3002\u82e5\u5728\u8fd9\u4e2a\u57fa\u56e0\u7ec4\u6ca1\u6709\u8fd9\u6837\u7684pairs\uff0c\u5219\u8be5\u57fa\u56e0\u7ec4\u6240\u6709\u7684in-paralog pairs\u90fd\u4e3a\u6709\u6548\u7684in-paalog pairs\u3002\u6700\u540e\u5f97\u5230\u6240\u6709\u57fa\u56e0\u7ec4\u6240\u6709\u6709\u6548\u7684in-paralog pairs\u3002\u7136\u540e\u53d6\u8fd9\u4e9b\u6709\u6548in-paralog pairs\u7684weight\u7684\u5e73\u5747\u503c\u3002\u6700\u540e\uff0c\u6bcf\u4e2ain-paralog pair\u7684evalue\u6807\u51c6\u5316\u540e\u7684\u503c\u4e3a\u5176weight\u9664\u4ee5average weight\u3002 2. \u5bf9\u4e8eortholog\u6216co-ortholog pairs\u5219\u7b80\u5355\u5f88\u591a\uff0c\u6c42\u6240\u6709weight\u7684\u5e73\u5747\u503c\uff0c\u7136\u540e\u4f7f\u7528\u5404\u4e2apair\u7684weight\u9664\u4ee5average weight\uff0c\u5219\u5c06\u5176\u6807\u51c6\u5316\u4e86\u3002<\/p>\n

6. \u7f51\u7edc\u7248\u7684OrthoMCL\u7684\u4f7f\u7528<\/h1>\n

OrthoMCL-DB\u5df2\u7ecf\u5bf9150\u4e2aproteomes\u8fdb\u884c\u4e86OrthoMCL\u7684\u5206\u6790\uff0c\u5bf9orthologs\u8fdb\u884c\u4e86\u805a\u7c7b\u3002\u8fd9\u4e2a\u8fc7\u7a0b\u7531\u4e8e\u6570\u636e\u91cf\u5927\uff0c\u56e0\u6b64\uff0c\u5728\u597d\u51e0\u767e\u7684CPU\u8d44\u6e90\u4e0b\u4e5f\u9700\u8981\u597d\u51e0\u4e2a\u661f\u671f\u624d\u80fd\u505a\u5b8c\u3002
\n\u5728OrthoMCL-DB\u4e0a\u4e0a\u8f7d a set of proteins,\u670d\u52a1\u5668\u5219\u4f1a\u5c06\u6240\u6709\u4e0a\u4f20\u7684proteins\u6bd4\u5bf9\u5230OrthoMCL-DB\u4e2d\u6240\u6709\u7684proteins\u4e0a\uff1b\u9009\u53d6evalue 1e-5\u548c50% match\u7684cutoff\uff1b\u7136\u540e\u5c06protein\u5f52\u7c7b\u5230\u5176top hit\u6240\u5bf9\u5e94\u7684protein\u7684\u7c7b\u4e0a\uff1b\u5982\u679ctop hit\u6240\u5bf9\u5e94\u7684proteins\u6ca1\u6709group\uff0c\u5219\u8be5protein\u5f52\u7c7b\u5230NO_GROUP\u3002
\n\u7136\u540e\uff0c\u518d\u5bf9\u4e0a\u4e00\u6b65cutoff\u6389\u7684proteins\u6765\u4f7f\u7528OrthoMCL-DB\u7684in-paralog\u7b97\u6cd5\u6765\u521b\u5efain-paralogs pairs,\u7136\u540e\u518d\u8fdb\u884cMCL\u7684\u805a\u7c7b\u3002
\n\u4f7f\u7528\u8be5\u65b9\u6cd5\uff0c\u6700\u540e\u5c06a set of proteins\u8fdb\u884c\u4e86\u540c\u6e90\u57fa\u56e0\u7684\u805a\u7c7b\uff0c\u4f46\u662f\u7f3a\u70b9\u5982\u4e0b:
\n1. \u8fd9\u79cd\u65b9\u6cd5\u662f\u5355\u5411\u6700\u4f73\uff0c\u6839\u636eprotein\u6bd4\u5bf9\u7684\u6700\u4f73\u7ed3\u679c\u53bb\u5f52\u7c7b\u5230\u5df2\u6709\u7684group\u4e2d\u53bb\u3002\u4f46\u662f\u53cd\u8fc7\u6765\uff0c\u6700\u4f73\u6bd4\u5bf9\u7ed3\u679c\u5bf9\u5e94\u7684protein\u4e0d\u4e00\u5b9a\u548cquery protein\u662f\u6700\u4f73\u7684\u3002\u8fd9\u548cOrthoMCL\u7684\u7b97\u6cd5\u662f\u6709\u51fa\u5165\u7684\uff0c\u6240\u4ee5\u8be5\u65b9\u6cd5\u7701\u4e86\u65f6\u95f4\uff0c\u4f46\u662f\u7ed3\u679c\u548c\u771f\u6b63\u7684\u7ed3\u679c\u662f\u6709\u4e00\u5b9a\u5dee\u522b\u7684\u3002
\n2. \u53ea\u4f7f\u7528cutoff\u540e\u5269\u4e0b\u7684proteins\u8fdb\u884cin-paralog\u5206\u6790\uff0c\u800c\u6ca1\u6709\u8fdb\u884c\u6240\u6709query proteins\u4e4b\u95f4\u7684in-paralog\u5206\u6790\u3002
\n3. \u6ca1\u6709ortholog pairs\u548cco-ortholog pairs\u7684\u4fe1\u606f\uff0c\u6ca1\u6cd5\u8fdb\u884c\u5355\u62f7\u8d1d\u540c\u6e90\u57fa\u56e0\u7684\u63d0\u53d6\u4e0e\u5206\u6790\u3002<\/p>\n

7. \u672c\u5730OrthoMCL\u7684\u4f7f\u7528<\/a><\/h1>\n

\u5bf9\u6307\u5b9a\u7684a set of proteomes\u8fdb\u884c\u540c\u6e90\u57fa\u56e0\u5206\u6790\uff0c\u5219\u4f7f\u7528\u672c\u5730\u7684OrthoMCL\u8fdb\u884c\u5206\u6790\u3002\u800c\u5b98\u7f51\u4e0d\u63d0\u4f9b\u8fd9\u79cd\u670d\u52a1\uff0c\u56e0\u4e3a\u6d88\u8017\u7684\u8ba1\u7b97\u673a\u8d44\u6e90\u8fc7\u5927\u3002<\/p>\n

8. \u6ce8\u610f\u4e8b\u9879<\/h1>\n

1. \u5e8f\u5217\u90fd\u662f\u4f7f\u7528protein\u5e8f\u5217\uff0c\u800c\u4e0d\u662fnucleotide\u5e8f\u5217\uff0c\u662f\u56e0\u4e3aprotein\u5e8f\u5217\u66f4\u7cbe\u786e\u3002
\n2. proteomes\u4e2d\u7684\u5e8f\u5217\u8981\u53bb\u9664\u53ef\u53d8\u526a\u5207\uff0c\u53ea\u7559\u53d6alternative proteins\u4e2d\u957f\u5ea6\u6700\u957f\u7684\u3002\u5426\u5219\u5728\u6709alternative proteins\u5b58\u5728\u7684\u60c5\u51b5\u4e0b\uff0c\u5219\u4f1a\u9020\u6210pseudo-in-paralogs\uff08\u5373alternative proteins\u79f0\u4e3ain-paralogs\uff09\uff0c\u7ed9\u540e\u7eed\u7684\u5206\u6790\u9020\u6210\u9ebb\u70e6\u3002
\n3. paralog\u5206\u4e3ain-paralog\u548cout-paralog\u3002in-paralog\u662f\u6307\u540c\u4e00\u4e2a\u7269\u79cd\u7684paralogs\u7684\u5206\u5316\u53d1\u751f\u5728\u7269\u79cd\u5206\u5316\u4e4b\u540e\uff0c\u8fd9\u6837\u7684\u8bdd\uff0c\u4ee3\u8868in-paralogs\u4e4b\u95f4\u7684\u5e8f\u5217\u76f8\u4f3c\u6027\u6bd4\u5176orthologs\u7684\u76f8\u4f3c\u6027\u8981\u9ad8\uff1b\u901a\u8fc7OrthoMCL\u7684\u539f\u7406\u53ef\u4ee5\u770b\u51fa\uff0c\u5f88\u597d\u5f97\u5230\u5206\u6790\u3002\u800cout-paralog\u662f\u6307paralogs\u7684\u5206\u5316\u53d1\u751f\u5728\u7269\u79cd\u5206\u5316\u4ee5\u524d\uff0c\u8fd9\u4ee3\u8868out-paralogs\u7684\u5e8f\u5217\u4e4b\u95f4\u7684\u76f8\u4f3c\u6027\u6bd4\u67d0\u4e00\u4e2a\u7269\u79cd\u7684orthologs\u7684\u76f8\u4f3c\u6027\u8981\u4f4e\uff1b\u8fd9\u6837\u662f\u5f88\u4e0d\u597d\u5206\u6790\u7684\uff0c\u56e0\u4e3a\u4e0d\u597d\u5b9a\u9608\u503c\uff0c\u6216\u8005\u5f97\u5230\u7684\u7ed3\u679c\u4e0d\u6613\u5f97\u4e0d\u5230\u5927\u4f17\u7684\u8ba4\u53ef\uff1bOrthoMCL\u4e5f\u6ca1\u8fdb\u884cout-paralog\u7684\u5206\u6790\uff1b\u5f53\u7136\uff0c\u4e5f\u53ef\u4ee5\u53ea\u5c06\u4e00\u4e2aquery proteome\u8f93\u5165\u5230orthomcl\u6765\u8fdb\u884c\u5206\u6790\uff0c\u5f97\u5230\u7684\u662f\u6240\u6709paralog\u5206\u6790\u7ed3\u679c\uff0c\u5305\u542b\u4e86out-paralog\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

1. OrthoMCL\u7684\u7528\u9014 \u57fa\u4e8e\u5e8f\u5217\u7684\u76f8\u4f3c\u6027\uff0cOrthoMCL\u80fd\u5c06\u4e00\u7ec4prot … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[65],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1839"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1839"}],"version-history":[{"count":13,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1839\/revisions"}],"predecessor-version":[{"id":1855,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1839\/revisions\/1855"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1839"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1839"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1839"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}