{"id":1344,"date":"2013-05-29T17:20:53","date_gmt":"2013-05-29T09:20:53","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1344"},"modified":"2013-05-29T18:06:52","modified_gmt":"2013-05-29T10:06:52","slug":"%e4%bd%bf%e7%94%a8evm%e6%95%b4%e5%90%88%e5%9f%ba%e5%9b%a0%e9%a2%84%e6%b5%8b%e7%bb%93%e6%9e%9c","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1344","title":{"rendered":"\u4f7f\u7528EVM\u6574\u5408\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c"},"content":{"rendered":"

1. EVM\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n

\u4eceEVM-sourceforge-download<\/a>\u4e2d\u4e0b\u8f7dEVM\uff0c\u5e76\u89e3\u538b\u7f29\u540e\u76f4\u63a5\u7528\u4e8eEVM\u7684\u4f7f\u7528\u3002<\/p>\n

2. EVM\u7684\u4f7f\u7528\u6b65\u9aa4<\/h1>\n

2.1 \u6536\u96c6gff3\u683c\u5f0f\u7684\u57fa\u56e0\u6ce8\u91ca\u5185\u5bb9<\/h2>\n

\u5728EVM\u4e2d\uff0c\u57fa\u56e0\u6ce8\u91ca\u5206\u4e3a3\u79cd\uff0c\u5e76\u5c06\u6240\u6709\u7684\u6ce8\u91ca\u4fe1\u606f\uff08\u65e0\u8bba\u4f7f\u7528\u90a3\u79cd\u65b9\u6cd5\u8fdb\u884c\u6ce8\u91ca\u7684\uff09\u5f52\u5165\u52303\u4e2a\u6587\u4ef6\u4e2d\uff1agene_predictions.gff3\u3001protein_alignments.gff3 \u548c transcript_alignments.gff3 \u8fd9\u4e09\u4e2a\u6587\u4ef6\u4e2d\u3002\u5f53\u7136\u8fd9\u4e09\u4e2a\u6587\u4ef6\u7684\u540d\u79f0\u53ef\u4ee5\u662f\u5176\u5b83\u7684\u540d\u5b57\uff0c\u4f46\u662fEVM\u53ea\u662f\u63a5\u53d7\u8fd93\u79cd\u6587\u4ef6\u3002<\/p>\n

\r\n$ cat genemark_hmm.gff3 snap.gff3 aug2.out.gfff3 > gene_predictions.gff3\r\n$ cat LEdodesGGTrinity.pasa_assemblies.gff3 > transcript_alignments.gff3\r\n$ perl -p -i -e 's\/^#.*\/\/s' gene_predictions.gff3 transcript_alignments.gff3\r\n<\/pre>\n
2.2 \u5236\u4f5cEvidence Weights File<\/h2>\n
3\u79cd\u6ce8\u91ca\u4fe1\u606f\u6709\u8fd9\u4e0d\u540c\u7684\u53ef\u4fe1\u5ea6\u3002\u4f9d\u9760\u81ea\u5df1\u7684\u76f4\u89c9\u6765\u8bbe\u7f6e\u4e0d\u540c\u6ce8\u91ca\u4fe1\u606f\u7684\u6743\u91cd\u3002\u7531\u4e8ePASA\u662f\u4f9d\u8d56\u4e8e\u8f6c\u5f55\u4fe1\u606f\u7684\uff0c\u5176\u6743\u91cd\u9ad8\uff1b\u800cab initio\u9884\u6d4b\u7684\u5219\u8981\u4f4e\u3002<\/p>\n
\u6bd4\u5982\uff1a\u6211\u4f7f\u7528\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u7684\u6570\u636e\u8fdb\u884c\u4e86PASA\u9884\u6d4b\uff1b\u901a\u8fc7PASA\u7684\u7ed3\u679c\uff0c\u4f7f\u7528Augustus\u6784\u5efaHMM\u6a21\u578b\uff0c\u7ed3\u5408\u8f6c\u5f55\u7ec4\u6570\u636e\u6784\u5efahints\u6765\u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\uff1b\u901a\u8fc7PASA\u7ed3\u679c\uff0c\u4f7f\u7528SNAP\u6765\u6784\u5efaHMM\u6a21\u578b\uff0c\u8fdb\u884cab initio\u57fa\u56e0\u9884\u6d4b\uff1b\u4f7f\u7528GeneMark_ES\u8fdb\u884c\u81ea\u6211\u8bad\u7ec3\u5efa\u6a21\u6765ab initio\u57fa\u56e0\u9884\u6d4b\u3002<\/p>\n
\u4ee5\u4e0a4\u4e2d\u65b9\u6cd5\u4e2d\uff0c\u5206\u522b\u7684\u6743\u91cd\u503c\u5219\u662f\uff1aPASA > Augustus > SNAP > GeneMark_ES\u3002<\/p>\n
\u4e00\u822c\u7684\u5efa\u8bae\u662f\uff1a weight(pasa) >> weight (protein) >= weight(prediction)<\/p>\n
\u7531\u4e8e\u4f7f\u7528\u4e86\u8f6c\u5f55\u7ec4\u7684\u6570\u636e\uff0c\u6211\u5bf9\u4ee5\u4e0a4\u4e2a\u9884\u6d4b\u65b9\u6cd5\u7684\u6743\u91cd\u662f\uff1a<\/p>\n
\r\necho \"ABINITIO_PREDICTION   AUGUSTUS    6\r\nABINITIO_PREDICTION GeneMark.hmm    1\r\nABINITIO_PREDICTION SNAP    2\r\nTRANSCRIPT  assembler-LEdodesGGTrinity  10\" > weights.txt\r\n<\/pre>\n
\u8be5\u6743\u91cd\u6587\u4ef6\u683c\u5f0f\u4e3a\uff1a\u4e09\u5217\uff1b\u7b2c\u4e00\u5217\u6709\u4e09\u79cd\uff0c\u5206\u522b\u662fABINITIO_PREDICTION\u3001PROTEIN \u548c TRANSCRIPT\uff1b\u7b2c\u4e8c\u5217\u662fgff3\u6587\u4ef6\u4e2d\u5bf9\u5e94\u7684type\u4e00\u5217\uff0c\u5373gff3\u6587\u4ef6\u7684\u7b2c3\u5217\uff1b\u7b2c3\u5217\u5219\u662f\u6743\u91cd\u5927\u5c0f\u3002<\/p>\n
3.3 \u5236\u4f5cPASA-supported terminal exons supplement<\/h2>\n
\u8be5\u7ec8\u6b62\u5916\u663e\u5b50\u7684\u4fe1\u606f\u6587\u4ef6\uff0c\u662f\u53ef\u9009\u7684\uff0c\u5e76\u63a8\u8350\u4f7f\u7528\u3002\u4f46\u662f\u53ef\u80fd\u7531\u4e8ePASA\u6700\u65b0\u7248\u672c\u7684\u7a0b\u5e8f\u548cEVM\u4f7f\u7528\u6587\u6863\u4e2d\u7684\u63cf\u8ff0\u7684\u4e0d\u4e00\u81f4\uff0c\u8be5\u6587\u4ef6\u7684\u5236\u4f5c\uff0c\u6709\u70b9\u96be\u5ea6\u3002\u6700\u540e\u5236\u4f5c\u51fa\u6765\u4e86\uff0c\u4f7f\u7528\u8be5\u6587\u4ef6\u7684\u65f6\u5019\uff0c\u5374\u662f\u7a0b\u5e8f\u4e0d\u80fd\u8fd0\u884c\u3002\u9700\u8981\u518d\u6b21\u6478\u7d22\u3002\u5c31\u4e0d\u9610\u8ff0\u4e86\u3002\u7565\u8fc7\u8be5\u6b65\u9aa4\u5373\u53ef\u3002<\/p>\n
3.4 \u8fd0\u884cEVM\u7684\u5206\u5757\u7a0b\u5e8f<\/h2>\n
\u4f7f\u7528 partition_EVM_inputs.pl \u7a0b\u5e8f\u5c06\u8f93\u5165\u7684\u9700\u8981\u9884\u6d4b\u7684scaffolds[\u6216chromosomes\u3001contigs]\u5206\u5f00\u5230\u5355\u72ec\u7684\u6587\u4ef6\u5939\u4e2d\u3002\u7ed3\u679c\u5f97\u5230\u5f88\u591a\u4e2a\u6587\u4ef6\u5939\uff0c\u6bcf\u4e2a\u6587\u4ef6\u5939\u5bf9\u5e941\u6761\u5e8f\u5217\uff0c\u4ee5\u53ca\u76f8\u5e94\u7684gff3\u6ce8\u91ca\u4fe1\u606f;\u540c\u65f6\u4e5f\u5f97\u5230\u4e86\u4e00\u4e2a\u5206\u5757\u7684\u4fe1\u606f\u6587\u4ef6\u3002\u8be5\u7a0b\u5e8f\u7684\u8fd0\u884c\u548c\u53c2\u6570\u4e3a\uff1a<\/p>\n
\r\n$ $EVMHome\/EvmUtils\/partition_EVM_inputs.pl --genome genome.fasta --gene_predictions gene_predictions.gff3 --transcript_alignments transcript_alignments.gff3 --segmentSize 500000 --overlapSize 10000 --partition_listing partitions_list.out\r\n\r\n--genome                * :fasta file containing all genome sequences\r\n--gene_predictions      * :file containing gene predictions\r\n--protein_alignments      :file containing protein alignments\r\n--transcript_alignments   :file containing transcript alignments\r\n--pasaTerminalExons       :file containing terminal exons based on PASA long-orf data.\r\n--repeats                 :file containing repeats to be masked\r\n--segmentSize           * :length of a single sequence for running EVM\r\n--overlapSize           * :length of sequence overlap between segmented sequences\r\n--partition_listing     * :name of output file to be created that contains the list of partitions\r\n-h                        : help message with more detailed information.\r\n(*required options)\r\n<\/pre>\n
3.5 \u751f\u6210EVM\u547d\u4ee4<\/h2>\n
\u4e0a\u4e00\u6b65\u751f\u6210\u4e86\u5f88\u591a\u6587\u4ef6\u5939\uff0c\u8fd9\u4e00\u6b65\u5bf9\u6bcf\u4e2a\u6587\u4ef6\u5939\u751f\u6210\u4e00\u4e2aEVM\u8fd0\u884c\u7684\u547d\u4ee4\uff0c\u5e76\u5c06\u8fd9\u4e9b\u547d\u4ee4\u653e\u5165\u7684\u6587\u4ef6commands.list\u4e2d\u3002<\/p>\n
\r\n$ $EVMHome\/EvmUtils\/write_EVM_commands.pl --genome genome.fasta --gene_predictions gene_predictions.gff3 --transcript_alignments transcript_alignments.gff3 --weights `pwd`\/weights.txt --output_file_name evm.out partitions_list.out > commands.list\r\n<\/pre>\n
3.6 \u6267\u884ccommands.list\u4e2d\u7684\u547d\u4ee4<\/h2>\n
\u5bf9\u4e8e\u8fd9\u4e9b\u547d\u4ee4\uff0c\u53ef\u4ee5\u4f7f\u7528\u8ba1\u7b97\u673a\u96c6\u7fa4\u8fdb\u884c\u591a\u7ebf\u7a0b\u7684\u8fd0\u7b97\uff1b\u5f53\u7136\u4e5f\u80fd\u5c06\u8fd9\u4e9b\u547d\u4ee4\u62c6\u6210\u591a\u4efd\uff0c\u4e00\u8d77\u8fd0\u7b97\uff0c\u4e5f\u5c31\u662f\u591a\u7ebf\u7a0b\u7684\u4e86\uff1b\u53ef\u4ee5\u4f7f\u7528EVM\u81ea\u5e26\u7684\u4e00\u4e2a\u7a0b\u5e8f\u6765\u8fd0\u884c\uff0c\u8fd9\u6837\u6709\u597d\u7684\u7ed3\u679c\u5c55\u793a\u3002\u591a\u7ebf\u7a0b\u8fd0\u884c\u80fd\u8282\u7ea6\u65f6\u95f4\u3002\u6bcf\u4e2a\u547d\u4ee4\u7684\u6267\u884c\u540e\u80fd\u5728\u5bf9\u5e94\u7684\u6587\u4ef6\u5939\u751f\u6210\u4e00\u4e2a\u540d\u4e3a evm.out \u7684\u7ed3\u679c\u6587\u4ef6(\u4e0a\u4e00\u6b65\u7684–output_file_name\u53c2\u6570\u7684\u8bbe\u5b9a)\u3002<\/p>\n
\r\n$EVMHome\/EvmUtils\/execute_EVM_commands.pl commands.list | tee run.log\r\n<\/pre>\n
3.7 \u548c\u5e76EVM\u7684\u6587\u4ef6<\/h2>\n
\u5c06\u6bcf\u4e2a\u6587\u4ef6\u5939\u4e2d\u7684EVM\u8f93\u51fa\u7ed3\u679c\u6587\u4ef6\u8fdb\u884c\u5408\u5e76\uff0c\u5f97\u5230\u6700\u540e\u7684gff3\u6587\u4ef6\u3002<\/p>\n
\r\n$EVMHome\/\r\nEvmUtils\/convert_EVM_outputs_to_GFF3.pl --partitions partitions_list.out --output_file_name evm.out --genome genome.fasta\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. EVM\u4e0b\u8f7d\u548c\u5b89\u88c5 \u4eceEVM-sourceforge-download\u4e2d\u4e0b\u8f7d … \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":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1344"}],"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=1344"}],"version-history":[{"count":5,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1344\/revisions"}],"predecessor-version":[{"id":1350,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1344\/revisions\/1350"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1344"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1344"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1344"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}