{"id":1212,"date":"2013-05-07T01:24:15","date_gmt":"2013-05-06T17:24:15","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1212"},"modified":"2013-05-11T16:32:32","modified_gmt":"2013-05-11T08:32:32","slug":"gene-structure-prediction-methods","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1212","title":{"rendered":"gene structure prediction methods"},"content":{"rendered":"<p>\u57fa\u56e0\u9884\u6d4b\u7684\u65b9\u6cd5\u6709\u5f88\u591a\u3002\u7ef4\u57fa\u767e\u79d1\uff1a<a href=\"http:\/\/en.wikipedia.org\/wiki\/List_of_gene_prediction_software\" target=\"_blank\">http:\/\/en.wikipedia.org\/wiki\/List_of_gene_prediction_software<\/a>\uff1b<a href=\"http:\/\/www.geneprediction.org\" target=\"_blank\">http:\/\/www.geneprediction.org<\/a>\u4e0a\u63d0\u4f9b\u4e86\u5927\u91cf\u7684\u57fa\u56e0\u9884\u6d4b\u7684\u8f6f\u4ef6\u548c\u6307\u5bfc\u4e66\u7c4d<\/p>\n<p>\u4ee5\u4e0b\u4ecb\u7ecd\u4e3b\u8981\u7684\u771f\u6838\u751f\u7269\u57fa\u56e0\u9884\u6d4b\u7684\u51e0\u4e2a\u65b9\u6cd5\uff1a<\/p>\n<h1>1. <a href=\"http:\/\/bioinf.uni-greifswald.de\/augustus\/\" target=\"_blank\">Augustus<\/a><\/h1>\n<p>AUGUSTUS ususally belongs to the most accurate programs for the species it is trained for. Often it is the most accurate ab initio program. <\/p>\n<p>AUGUSTUS\u7684\u53d1\u5c55\u5f88\u5feb\uff0c\u7248\u672c\u4e0d\u65ad\u66f4\u65b0\uff0c\u529f\u80fd\u8d8a\u6765\u8d8a\u5b8c\u5584\u3002AUGUSTUS\u80fd\u5f88\u597d\u5730\u7ed3\u5408RNA-seq\u6570\u636e\u5f97\u5230\u7684hints.gff\u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\u3002<\/p>\n<h1>2. <a href=\"http:\/\/exon.biology.gatech.edu\/\" target=\"_blank\">GeneMark-ES<\/a><\/h1>\n<p>GeneMark-ES\u4f7f\u7528\u8d77\u6765\u6700\u7b80\u5355\uff0c\u552f\u4e00\u7684\u80fd\u4ee5\u57fa\u56e0\u7ec4\u81ea\u6211\u8bad\u7ec3\u51fa\u8bad\u7ec3\u96c6\u7528\u4e8e\u57fa\u56e0\u9884\u6d4b\u3002\u8be5\u8f6f\u4ef6\u4e0d\u63d0\u4f9b\u4f7f\u7528\u5df2\u6709\u6a21\u578b\u6765\u9884\u6d4b\u57fa\u56e0\u3002\u5bf9\u5e94\u7684\u4f7f\u7528\u6a21\u578b\u7684\u7248\u672c\u4e3aGeneMark.hmm eukaryotic\uff0c\u4f46\u662f\u80fd\u4f7f\u7528\u7684\u6a21\u578b\u592a\u5c11\uff0c\u4e0d\u63d0\u4f9b\u5176\u5efa\u6a21\u7684\u65b9\u6cd5\u3002<\/p>\n<h1>3. <a href=\"http:\/\/linux1.softberry.com\/berry.phtml?topic=index&#038;group=programs&#038;subgroup=gfind\" target=\"_blank\">FGENESH<\/a><\/h1>\n<p>FGENSH\u662f\u5546\u4e1a\u8f6f\u4ef6\uff0c\u7531Softberry\u516c\u53f8\u8d1f\u8d23\u7ef4\u62a4\u548c\u53d1\u5e03\uff0c\u7528\u6237\u53ea\u80fd\u8054\u7f51\u5c0f\u91cf\u4f7f\u7528\u3002\u82e5\u9700\u8981\u5927\u91cf\u4f7f\u7528\u6216\u672c\u5730\u5316\u8fd0\u884c\uff0c\u5219\u9700\u8981\u4ed8\u8d39\u3002\u627e\u4e86\u534a\u5929\uff0c\u5b98\u7f51\u4e0d\u63d0\u4f9b\u8f6f\u4ef6\u7684\u4e0b\u8f7d\u3002\u4f7f\u7528\u7f51\u9875\u7248\u7684FGENESH\u53bb\u8fdb\u884c\u57fa\u56e0\u7ec4\u57fa\u672c\u7684\u57fa\u56e0\u9884\u6d4b\uff0c\u5f88\u957f\u65f6\u95f4\u540e\u8fd4\u56de\u9519\u8bef\uff1aRequest not processed   413 Request entity too large\u3002<\/p>\n<h1>4. <a href=\"http:\/\/www.mgene.org\/\" target=\"_blank\">mGene[.web]<\/a><\/h1>\n<p>\u867d\u7136\u662f\u65b0\u8fd1\u7684\u8f6f\u4ef6\uff0c\u4f46\u662f\u8be5\u8f6f\u4ef6\u73b0\u5728\u8fd8\u4e0d\u6210\u719f\uff0c\u4f7f\u7528\u4e0d\u6613\u3002\u8be5\u8f6f\u4ef6\u7cbe\u786e\u5ea6\u8c8c\u4f3c\u8f83\u9ad8\uff0c\u7279\u522b\u662f\u5728\u4e0b\u7ebf\u866b\u4e2d\uff0c\u548cAugustus\u5dee\u4e0d\u591a\u4e86\u3002<\/p>\n<h1>5. <a href=\"http:\/\/korflab.ucdavis.edu\/software.html\" target=\"_blank\">SNAP<\/a><\/h1>\n<p><a href=\"http:\/\/korflab.ucdavis.edu\/bio_ian.html\" target=\"_blank\">Ian Korf<\/a>\u72ec\u81ea\u5199\u4e86\u8be5\u8f6f\u4ef6\uff0c2004\u5e74\u53d1\u8868\u5728BMC Bioinformatics\u4e0a\uff0c\u5f15\u7528\u6b21\u6570208.<\/p>\n<p>\u8be5\u8f6f\u4ef6\u5b89\u88c5\u7b80\u5355\uff0c\u8f6f\u4ef6\u8bf4\u660e\u8f83\u5c11\uff0c\u4f5c\u8005\u53ea\u662f\u7b80\u5355\u5728README\u4e2d\u63d0\u5230\u600e\u4e48\u53bb\u5efaHMM\u7684\u6a21\u578b\u3002<\/p>\n<h1>6. <a href=\"http:\/\/ccb.jhu.edu\/software\/glimmerhmm\/\" target=\"_blank\">Glimmer[HMM]<\/a><\/h1>\n<p>\u4f7f\u7528Glimmerhmm\uff0c\u5e94\u8be5\u8fd8\u4e0d\u5982\u4f7f\u7528SNAP\u3002<\/p>\n<h1>7. <a href=\"http:\/\/genome.crg.es\/software\/geneid\/index.html\" target=\"_blank\">geneid<\/a><\/h1>\n<p>geneid\u7684<a href=\"http:\/\/genome.crg.es\/software\/geneid\/training.html\" target=\"_blank\">training\u7684\u6587\u6863<\/a>\u4e2d\u5199\u5f97\u5f88\u662f\u7e41\u7410\uff0c\u4e0d\u60f3\u770b\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u57fa\u56e0\u9884\u6d4b\u7684\u65b9\u6cd5\u6709\u5f88\u591a\u3002\u7ef4\u57fa\u767e\u79d1\uff1ahttp:\/\/en.wikipedia.org\/ &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1212\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1212"}],"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=1212"}],"version-history":[{"count":13,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1212\/revisions"}],"predecessor-version":[{"id":1219,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1212\/revisions\/1219"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1212"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1212"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1212"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}