{"id":2804,"date":"2019-04-14T20:39:59","date_gmt":"2019-04-14T12:39:59","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2804"},"modified":"2019-04-16T14:37:38","modified_gmt":"2019-04-16T06:37:38","slug":"%e4%bd%bf%e7%94%a8eggnog%e6%95%b0%e6%8d%ae%e5%ba%93%e8%bf%9b%e8%a1%8c%e5%9f%ba%e5%9b%a0%e5%8a%9f%e8%83%bd%e6%b3%a8%e9%87%8a","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2804","title":{"rendered":"\u4f7f\u7528eggNOG\u6570\u636e\u5e93\u8fdb\u884c\u57fa\u56e0\u529f\u80fd\u6ce8\u91ca"},"content":{"rendered":"\n<h2>1. EggNOG\u6570\u636e\u5e93\u7b80\u4ecb<\/h2>\n\n\n\n<p><a rel=\"noreferrer noopener\" aria-label=\"eggNOG ( Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups) \u516c\u5171\u6570\u636e\u5e93V5.0\u7248\u672c\uff08\u5728\u65b0\u7a97\u53e3\u6253\u5f00\uff09\" href=\"http:\/\/eggnog5.embl.de\/\" target=\"_blank\">eggNOG ( Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups) \u516c\u5171\u6570\u636e\u5e93V5.0\u7248\u672c<\/a>\u641c\u96c6\u4e865090\u4e2a\u751f\u7269\uff08477\u771f\u6838\u751f\u7269\u30014445\u4e2a\u4ee3\u8868\u6027\u7ec6\u83cc\u548c168\u53e4\u83cc\uff09\u548c2502\u4e2a\u75c5\u6bd2\u7684\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\u3002\u5c06\u8fd9\u4e9b\u7269\u79cd\u5206\u6210\u4e86<a rel=\"noreferrer noopener\" aria-label=\"379\u7c7b\uff08taxonomic levels\uff09\uff08\u5728\u65b0\u7a97\u53e3\u6253\u5f00\uff09\" href=\"http:\/\/eggnog5.embl.de\/#\/app\/downloads\" target=\"_blank\">379\u7c7b\uff08taxonomic levels\uff09<\/a>\uff0c\u6bcf\u7c7b\u7684\u7f16\u53f7\u4ee5NCBI\u7684\u5206\u7c7b\u7f16\u53f7\u8868\u793a\uff0c\u4f8b\u5982<a href=\"http:\/\/eggnog5.embl.de\/download\/eggnog_5.0\/per_tax_level\/4751\/\" target=\"_blank\" rel=\"noreferrer noopener\" aria-label=\"fungi\u7684\u7f16\u53f74751\uff08\u5728\u65b0\u7a97\u53e3\u6253\u5f00\uff09\">fungi\u7684\u7f16\u53f74751<\/a>\u3002\u5bf9\u5404\u4e2a\u7c7b\u522b\u7269\u79cd\u7684\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u540c\u6e90\u57fa\u56e0\u5206\u7c7b\uff0c\u603b\u5171\u5f97\u52304.4M\u4e2a\u540c\u6e90\u57fa\u56e0\u7c7b\uff08orthologous groups \/ OGs\uff09\u3002\u5bf9\u6bcf\u4e2a\u540c\u6e90\u57fa\u56e0\u7c7b\u8fdb\u884c\u4e86\u591a\u5e8f\u5217\u6bd4\u5bf9\u3001\u7cfb\u7edf\u53d1\u80b2\u6811\u6784\u5efa\u3001HMM\u6587\u4ef6\u6784\u5efa\u548c\u529f\u80fd\u6ce8\u91ca\u3002<\/p>\n\n\n\n<p>eggNOG\u6570\u636e\u5e93\u662fNCBI\u7684COG\u6570\u636e\u5e93\u7684\u6269\u5c55\uff0c\u5b83\u6536\u96c6\u4e86\u66f4\u5168\u9762\u7684\u7269\u79cd\u548c\u66f4\u5927\u91cf\u7684\u86cb\u767d\u5e8f\u5217\u6570\u636e\u3002\u540c\u6837\u8fdb\u884c\u4e86\u540c\u6e90\u57fa\u56e0\u805a\u7c7b\u5206\u6790\u548c\u5bf9\u6bcf\u4e2a\u540c\u6e90\u57fa\u56e0\u7c7b\u7684\u63cf\u8ff0\u548c\u529f\u80fd\u5206\u7c7b\u3002eggNOG\u66f4\u5f3a\u5927\u7684\u529f\u80fd\u5728\u4e8e\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">1. \u5bf9\u66f4\u5168\u9762\u7684\u7269\u79cd\u548c\u66f4\u5927\u91cf\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u5206\u7c7b\u3002\u76f8\u6bd4\u4e8eCOG\u6570\u636e\u5e93\u7eaf\u4eba\u5de5\u4e14\u8f83\u4e3a\u51c6\u786e\u7684\u5206\u7c7b\uff0ceggNOG\u6570\u636e\u5e93\u6269\u5927\u7269\u79cd\u548c\u5e8f\u5217\u6570\u636e\u91cf\uff0c\u91c7\u7528\u4e86\u975e\u76d1\u7763\u805a\u7c7b\u65b9\u6cd5\u8fdb\u884c\u8ba1\u7b97\u3002<br>2. \u5bf9\u6bcf\u4e2a\u540c\u6e90\u57fa\u56e0\u7c7b\u8fdb\u884c\u4e86\u7cfb\u7edf\u53d1\u80b2\u6811\u6784\u5efa\u3001HMM\u6a21\u578b\u6784\u5efa\u3001GO\u6ce8\u91ca\u3001KEGG Pathway\u6ce8\u91ca\u3001SMART\/FPAM\u7ed3\u6784\u57df\u6ce8\u91ca\u3001CAZyme\u6ce8\u91ca\u7b49\u3002<br>3. \u63d0\u4f9b\u4e86\u672c\u5730\u5316\u8f6f\u4ef6\u548c\u7f51\u9875\u5de5\u5177\u8fdb\u884ceggNOG\u6ce8\u91ca\u3002<\/pre>\n\n\n\n<p>eggNOG\u6570\u636e\u5e93\u7684\u5bf9379\u7c7b\u7269\u79cd\uff0c\u6bcf\u7c7b\u7269\u79cd\u90fd\u751f\u6210\u5176\u6570\u636e\u5e93\u6587\u4ef6\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">0. <a rel=\"noreferrer noopener\" aria-label=\"e5.proteomes.faa\u6587\u4ef6\uff08\u5728\u65b0\u7a97\u53e3\u6253\u5f00\uff09\" href=\"http:\/\/eggnog5.embl.de\/download\/eggnog_5.0\/\" target=\"_blank\">e5.proteomes.faa\u6587\u4ef6<\/a>\uff1a\u6536\u96c6\u6240\u6709\u7269\u79cd\u7684\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\u6587\u4ef6\u3002\u4e00\u4e2a\u603b\u7684\u6570\u636e\u5e93\u6587\u4ef6\u3002<br><br>1. members\u6587\u4ef6\uff1a\u8bb0\u5f55OG\u7f16\u53f7\u53ca\u5bf9\u5e94\u7684\u86cb\u767d\u5e8f\u5217\u767b\u5f55\u53f7\u3002\u7f16\u5199\u7a0b\u5e8f\u53ef\u4ee5\u4ece0\u53f7\u6587\u4ef6\u4e2d\u63d0\u53d6\u76ee\u6807\u7c7b\u7684\u86cb\u767d\u5e8f\u5217\u6570\u636e\u3002<br>2. annotations\u6587\u4ef6\uff1a\u8bb0\u5f55OG\u7f16\u53f7\u7684\u63cf\u8ff0\u4fe1\u606f\u53ca\u6240\u5c5e\u5927\u7c7b\u4fe1\u606f\u3002<br>3. hmms\u6587\u4ef6\uff1a\u5df2\u7ecf\u6784\u5efa\u597d\u7684hmm\u6570\u636e\u5e93\u6587\u4ef6\u3002<br><br>4. raw_algs\u6587\u4ef6\uff1a\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6<br>5. trimmed_algs\u6587\u4ef6\uff1a\u622a\u77ed\u540e\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6<br>6. tress\u6587\u4ef6\uff1a\u7edf\u53d1\u80b2\u6811\u6587\u4ef6\u3002<br>7. stats\u6587\u4ef6\uff1a\u7edf\u8ba1\u540c\u6e90\u57fa\u56e0\u7c7b\u7684\u4e2a\u6570\u3002<br><\/pre>\n\n\n\n<h2>2. \u4f7f\u7528<a rel=\"noreferrer noopener\" aria-label=\"\u7f51\u9875\u5de5\u5177\uff08\u5728\u65b0\u7a97\u53e3\u6253\u5f00\uff09\" href=\"http:\/\/eggnogdb.embl.de\/#\/app\/emapper\" target=\"_blank\">\u7f51\u9875\u5de5\u5177<\/a>\u8fdb\u884ceggNOG\u6ce8\u91ca<\/h2>\n\n\n\n<p>\u76ee\u524d\uff0820190414\uff09\uff0ceggNOG\u867d\u7136\u63d0\u4f9b\u4e86\u7b2c5\u7248\u6570\u636e\u4fe1\u606f\u7684\u4e0b\u8f7d\uff0c\u4f46\u662f\u7f51\u9875\u5de5\u5177\u4ec5\u63d0\u4f9b4.5.1\u7248\u672c\u7684\u5206\u6790\u3002\u7f51\u9875\u5de5\u5177\u652f\u6301DIAMOND\u548cHMMER\u4e24\u79cd\u7b97\u6cd5\u8fdb\u884ceggNOG\u6ce8\u91ca\u3002\u867d\u7136HMMER\u65b9\u6cd5\u4e00\u822c\u51c6\u786e\u6027\u66f4\u9ad8\uff0c\u4f46\u4ec5\u652f\u6301\u5355\u6b21\u63d0\u4ea4\u4e0d\u8d85\u8fc75000\u6761\u5e8f\u5217\u7684FASTA\u6587\u4ef6\u3002<\/p>\n\n\n\n<p>\u63a8\u8350\u4f7f\u7528\u7f51\u9875\u5de5\u5177\u8fdb\u884ceggNOG\u6ce8\u91ca\uff0c\u7b80\u5355\u65b9\u4fbf\uff0c\u7ed3\u679c\u8ba4\u53ef\u5ea6\u9ad8\u3002\u4ee5\u4e0b\u60c5\u51b5\u63a8\u8350\u4f7f\u7528 <br>\u5b98\u65b9\u63d0\u4f9b\u7684\u8f6f\u4ef6eggnog-mapper\u8fdb\u884c\u672c\u5730\u5316\u6ce8\u91ca\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">\uff081\uff09\u6ce8\u91ca\u7684\u6570\u636e\u91cf\u8fc7\u5927\uff0c\u6bd4\u5982\u5b8f\u57fa\u56e0\u7ec4\u6570\u636e\uff1b<br>\uff082\uff09\u4f7f\u7528\u66f4\u51c6\u786e\u7684HMMER\u7b97\u6cd5\u4e00\u6b21\u6027\u6ce8\u91ca\u8d85\u8fc75000\u6761\u5e8f\u5217\uff1b<br>\uff083\uff09\u60f3\u66f4\u5feb\u5730\u8fdb\u884ceggNOG\u6ce8\u91ca\uff1b<br>\uff084\uff09\u7f51\u7edc\u6761\u4ef6\u8f83\u5dee\u3002<\/pre>\n\n\n\n<h2>3. \u4e0b\u8f7d\u5e76\u5b89\u88c5<a href=\"https:\/\/github.com\/eggnogdb\/eggnog-mapper\" target=\"_blank\" rel=\"noreferrer noopener\" aria-label=\"eggnog-mapper\uff08\u5728\u65b0\u7a97\u53e3\u6253\u5f00\uff09\">eggnog-mapper<\/a>\u8f6f\u4ef6\u548c\u6570\u636e\u5e93\u6587\u4ef6<\/h2>\n\n\n\n<p>\u5b89\u88c5eggnog-mapper\u8f6f\u4ef6\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ wget https:\/\/github.com\/eggnogdb\/eggnog-mapper\/archive\/1.0.3.tar.gz -O ~\/software\/eggnog-mapper-1.0.3.tar.gz\n$ tar zxf ~\/software\/eggnog-mapper-1.0.3.tar.gz -C \/opt\/biosoft\/\n$ cd \/opt\/biosoft\/eggnog-mapper-1.0.3\n$ python setup.py install\n$ echo 'PATH=$PATH:\/opt\/biosoft\/eggnog-mapper-1.0.3' >> ~\/.bashrc\n$ source ~\/.bashrc\n$ download_eggnog_data.py euk bact arch viruses\n    \u4e0b\u8f7deggNOG v4.5\u7248\u672c\u7684\u6570\u636e\u5e93\u6587\u4ef6eggnog.db\u548ceggnog_proteins.dmnd\uff0c\u5e76\u989d\u5916\u4e0b\u8f7d\u6307\u5b9a\u7684HMM\u6570\u636e\u5e93\u3002\u53ef\u4ee5\u6839\u636e\u9700\u8981\u9009\u62e9\u6307\u5b9a\u7684\u6570\u636e\u5e93\u5373\u53ef\uff0c\u4e0b\u8f7d\u591a\u4e2a\u6570\u636e\u5e93\u6d88\u8017\u66f4\u5927\u7684\u78c1\u76d8\u7a7a\u95f4\uff1a\u6bd4\u5982euk\u6d88\u801776G\u78c1\u76d8\u7a7a\u95f4\u3001bact\u6d88\u801726G\u78c1\u76d8\u7a7a\u95f4\u3001arch\u6d88\u80177G\u78c1\u76d8\u7a7a\u95f4\u3001viruses\u6d88\u8017468M\u78c1\u76d8\u7a7a\u95f4\u3002<\/code><\/pre>\n\n\n\n<p>\u5728eggnog-mapper\u8f6f\u4ef6\u5b89\u88c5\u76ee\u5f55\u4e0b\u7684data\u6587\u4ef6\u5939\u4e0b\u5b58\u653e\u6709\u6570\u636e\u5e93\u6587\u4ef6\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">eggnog_proteins.dmnd    \u6240\u6709\u86cb\u767d\u5e8f\u5217\u7684DIMOND\u6570\u636e\u5e93\uff0c\u7528\u4e8eDIMOND\u5feb\u901f\u5e8f\u5217\u6bd4\u5bf9<br>eggnog.db    \u529f\u80fd\u6ce8\u91ca\u6570\u636e\u5e93\uff0c\u7528\u4e8e\u6839\u636e\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca<br>hmmdb_levels\/    \u5b58\u653e\u6709\u5404\u4e2a\u7269\u79cd\u7c7b\u522b\u7684HMM\u6570\u636e\u5e93<br>OG_fasta\/    \u5b58\u653e\u5404\u4e2a\u7269\u79cd\u7c7b\u522b\u7684\u86cb\u767d\u5e8f\u5217\u6570\u636e\u5e93\u3002<br><\/pre>\n\n\n\n<h2>4. \u4f7f\u7528eggnog-mapper\u8f6f\u4ef6\u8fdb\u884ceggNOG\u6ce8\u91ca<\/h2>\n\n\n\n<p>eggnog-mapper\u8f6f\u4ef6\u8fd0\u884c\u7684\u539f\u7406\uff1a\uff081\uff09\u7a0b\u5e8f\u8c03\u7528HMMER\u7b97\u6cd5\u5c06query\u5e8f\u5217\u6bd4\u5bf9\u5230HMM\u6570\u636e\u5e93\uff0c\u5f97\u5230\u5339\u914d\u4e0a\u7684OGs\u7ed3\u679c\u3002\u7136\u540e\u5c06query\u5e8f\u5217\u548c\u6700\u4f18OG\u4e2d\u7684\u6240\u6709\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5f97\u5230\u6700\u4f18\u5339\u914d\u5e8f\u5217\uff08seed ortholog\uff09\u7ed3\u679c\u3002\uff082\uff09\u4e5f\u53ef\u4ee5\u9009\u62e9DIAMOND\u7b97\u6cd5\u5c06query\u5e8f\u5217\u6bd4\u5bf9\u5230\u86cb\u767d\u5e8f\u5217\u6570\u636e\u5e93\uff0c\u5f97\u5230\u6bd4\u5bf9\u7ed3\u679c\uff0c\u9009\u62e9\u6700\u4f18\u7684\u6bd4\u5bf9\u7ed3\u679c\u4f5c\u4e3aseed ortholog\u3002\uff083\uff09\u57fa\u4e8eeggNOG\u6570\u636e\u5e93\u4e2d\u7684\u5bf9\u5e94OG\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\uff0c\u6839\u636eseed ortholog\u80fd\u5f97\u5230\u8be6\u7ec6\u7684\u540c\u6e90\u57fa\u56e0\u8fdb\u5316\u5173\u7cfb\uff0c\u4ece\u800c\u5254\u9664\u4eb2\u7f18\u5173\u7cfb\u8f83\u8fdc\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\uff0c\u751a\u81f3\u53ef\u4ee5\u5254\u9664\u4e00\u5bf9\u591a\u7684\u540c\u6e90\u57fa\u56e0\u800c\u4ec5\u4fdd\u7559\u4e00\u5bf9\u4e00\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\uff0c\u5c06\u6700\u51c6\u786e\u7684\u540c\u6e90\u57fa\u56e0\u7684\u529f\u80fd\u6ce8\u91ca\u7ed3\u679c\u8f6c\u79fb\u7ed9query\u5e8f\u5217\uff0c\u4ece\u800c\u5bf9query\u5e8f\u5217\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca\u3002<\/p>\n\n\n\n<p>\u4f7f\u7528HMMER\u7b97\u6cd5\u8fdb\u884ceggNOG\u6ce8\u91ca\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>\u4f7f\u7528eggnog-mapper\u8f6f\u4ef6\uff0c\u63a8\u8350\u4f7f\u7528\u8f6f\u4ef6\u81ea\u5e26\u7684HMMER\u548cDIAMOND\u7a0b\u5e8f\u3002\u6211\u4f7f\u7528\u6700\u65b0\u7248\u672c\u7684HMMER\u8f6f\u4ef6\uff0c\u51fa\u73b0\u9519\u8bef\u63d0\u793a\uff1a\u201ctruct.error: unpack requires a string argument of length \u201d\u5e76\u5f97\u4e0d\u5230\u7ed3\u679c\u3002\n$ export PATH=\/opt\/biosoft\/eggnog-mapper-1.0.3\/bin\/:$PATH\n\n\u7531\u4e8eeggNOG\u6570\u636e\u5e93\u8f83\u5927\uff0c\u63a8\u8350\u5c06\u6570\u636e\u5e93\u653e\u5230\u5185\u5b58\u4e2d\uff0c\u4ee5\u52a0\u5feb\u7a0b\u5e8f\u8fd0\u884c\u901f\u5ea6\u3002\u9700\u8981\u6ce8\u610f\u7684\u662feuk\u6570\u636e\u6bd4\u8f83\u5927\uff0c\u6bd4\u8f83\u8d39\u5185\u5b58\uff0c\u5360\u7528\u4e86\u7ea6100G\u5185\u5b58\u5de6\u53f3\u3002\n$ emapper.py -d euk -i proteins.fasta -o eggNOG_hmmer --cpu 80 --usemem --no_file_comments\n\n\u82e5\u6709\u591a\u7ec4\u6570\u636e\u9700\u8981\u8fdb\u884ceggNOG\u6ce8\u91ca\uff0c\u53ef\u4ee5\u5206\u4e24\u6b65\u8fd0\u884c\u3002\u5148\u5c06\u6570\u636e\u5e93\u653e\u5230\u5185\u5b58\u4e2d\uff0c\u518d\u5206\u522b\u5bf9\u591a\u7ec4\u6570\u636e\u8fdb\u884c\u8fd0\u7b97\uff0c\u8fd9\u6837\u53ea\u8bfb\u53d6\u4e00\u6b21\u6570\u636e\u5e93\u5230\u5185\u5b58\u4e2d\u8282\u7ea6\u8fd0\u7b97\u65f6\u95f4\u3002\n$ emapper.py -d euk --cpu 80 --servermode\n\u5f85\u6570\u636e\u5e93\u52a0\u8f7d\u5b8c\u6bd5\u540e\uff0c\u53ef\u4ee5\u5728\u5176\u5b83\u7ec8\u7aef\u4e2d\u6267\u884c\u6570\u636e\u5206\u6790\u3002\n$ emapper.py -d euk:localhost:51400 -i proteins1.fasta -o eggNOG1 --no_file_comments\n$ emapper.py -d euk:localhost:51400 -i proteins2.fasta -o eggNOG2 --no_file_comments<\/code><\/pre>\n\n\n\n<p>\u4f7f\u7528DIAMOND\u7b97\u6cd5 \u8fdb\u884ceggNOG\u6ce8\u91ca \uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ python emapper.py -m diamond -i proteins.fasta -o eggNOG_diamond --cpu 80 --no_file_comments\n\n\u5206\u4e24\u6b65\u8fd0\u884cDIAMOND\u6bd4\u5bf9\u548c\u529f\u80fd\u6ce8\u91ca\u3002\u81ea\u5df1\u624b\u52a8\u8fd0\u884cDIAMOND\uff0c\u8bbe\u7f6e\u4e00\u4e9b\u6027\u80fd\u53c2\u6570\u548c\u4e25\u683c\u9608\u503c\u80fd\u66f4\u6709\u6548\u7387\u3002\n$ diamond blastp --db \/opt\/biosoft\/eggnog-mapper-1.0.3\/data\/eggnog_proteins --query proteins.fasta --out eggNOG.tab --outfmt 6 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 30 --block-size 20.0 --tmpdir \/dev\/shm --index-chunks 1\n$ parsing_blast_result.pl -type tab --max-hit-num 1 --db-query proteins.fasta --db-subject \/opt\/biosoft\/eggnog-mapper-1.0.3\/eggNOG_Database_5.0\/eggnog_proteins.fasta --HSP-num 1 eggNOG.tab | cut -f 1,2,11,12 > eggNOG.emapper.seed_orthologs\n$ perl -e '&lt;>; while (&lt;>) { print; }' eggNOG.emapper.seed_orthologs > aa; mv aa eggNOG.emapper.seed_orthologs\n$ emapper.py --annotate_hits_table eggNOG.emapper.seed_orthologs -o eggNOG<\/code><\/pre>\n\n\n\n<p>emapper.py\u7a0b\u5e8f\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\"><strong>\u8f93\u5165\u53c2\u6570\uff1a<br><\/strong>-h | --help<br>    \u6253\u5370\u5e2e\u52a9\u4fe1\u606f\u3002<br>-d | --database &lt;string><br>    \u8f93\u5165\u4f7f\u7528\u7684\u6570\u636e\u5e93\u540d\u79f0\u3002\u4e00\u822c\u9009\u62e9euk\uff0cbact\uff0carch\u3002\u6216\u8f93\u5165\u672c\u5730\u8ba1\u7b97\u673a\u4e0a\u7684HMM\u6570\u636e\u5e93\u8def\u5f84\u3002<br>-i &lt;string><br>    \u8f93\u5165query\u5e8f\u5217FASTA\u6587\u4ef6\u3002<br>--translate<br>    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u8ba4\u4e3a\u8f93\u5165\u7684FASTA\u6587\u4ef6\u662f\u6838\u9178\u5e8f\u5217\uff0c\u7a0b\u5e8f\u80fd\u5c06\u6838\u9178\u5e8f\u5217\u8f6c\u6362\u4e3a\u6c28\u57fa\u9178\u5e8f\u5217\u540e\u7528\u4e8e\u6bd4\u5bf9\u548c\u6ce8\u91ca\u3002<br>--annotate_hits_table &lt;string><br>    \u8f93\u5165seed ortholog\u6bd4\u5bf9\u4fe1\u606f\u3002\u8be5\u6587\u4ef6\u5206\u56db\u5217\uff1aqueryID\u3001subjectID\u3001evalue\u548cbit score\u3002\u8f93\u5165\u8be5\u4fe1\u606f\uff0c\u5219\u4e0d\u9700\u8981\u4f7f\u7528-i\u53c2\u6570\u8f93\u5165fasta\u6587\u4ef6\u4e86\uff0c\u7a0b\u5e8f\u76f4\u63a5\u8fd0\u884c\u6700\u540e\u4e00\u6b65\u529f\u80fd\u6ce8\u91ca\u3002<br>--data_dir &lt;string><br>    \u8f93\u5165eggNOG\u6570\u636e\u5e93\u6587\u4ef6\u6240\u5728\u7684\u8def\u5f84\u3002<br><br><strong>\u8f93\u51fa\u53c2\u6570\uff1a<br><\/strong>--output_dir &lt;string>    default: .\/<br>    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u5939\u3002<br>-o | --out &lt;string><br>    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u524d\u7f00\u3002<br>--resume<br>    \u6dfb\u52a0\u8be5\u53c2\u6570\u6765\u7ee7\u7eed\u8fd0\u884c\u7a0b\u5e8f\u3002<br>--override<br>    \u6dfb\u52a0\u8be5\u53c2\u6570\u8986\u76d6\u5df2\u6709\u7684\u7ed3\u679c\u6587\u4ef6\u3002<br>--no_search<br>    \u4e0d\u8fdb\u884cHMM\u6bd4\u5bf9\uff0c\u4f7f\u7528\u5df2\u6709\u7684HMM\u6bd4\u5bf9\u7ed3\u679c\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u7a0b\u5e8f\u4f7f\u7528HMMER\u7b97\u6cd5\u8fd0\u884c\u5206\u4e09\u6b65\uff1aHMM\u6bd4\u5bf9\u3001\u627eseed ortholog\u548c\u529f\u80fd\u6ce8\u91ca\u3002<br>--no_refine<br>    \u4e0d\u5229\u7528HMM\u7684\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884c\u5e8f\u5217\u6bd4\u5bf9\u5bfb\u627eseed ortholog\uff0c\u800c\u7ed3\u675f\u7a0b\u5e8f\uff0c\u4ec5\u4ec5\u62a5\u544aHMM\u6bd4\u5bf9\u7ed3\u679c\u3002<br>--no_annot<br>    \u4e0d\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca\uff0c\u4ec5\u62a5\u544aHMM\u548cseed ortholog\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002<br>--temp_dir &lt;string>    default: .\/<br>    \u8bbe\u7f6e\u4e34\u65f6\u6587\u4ef6\u5939\u8def\u5f84\u3002<br>--no_file_comments<br>    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u5728\u8f93\u51fa\u7ed3\u679c\u4e2d\u4e0d\u8f93\u51fa\u6ce8\u91ca\u884c\u4fe1\u606f\u3002\u63a8\u8350\u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u7a0b\u5e8f\u6709BUG\u5bb9\u6613\u5bfc\u81f4seed_ortholog\u6587\u4ef6\u4e2d\u542b\u6709#\u7684\u6ce8\u91ca\u884c\u51fa\u73b0\u5728\u7ed3\u679c\u4e2d\u90e8\uff0c\u5bfc\u81f4\u7a0b\u5e8f\u8fd0\u884c\u5931\u8d25\u3002<br>--keep_mapping_files<br>    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u4e0d\u5220\u9664\u4e2d\u95f4\u6587\u4ef6\u4e2d\u7684HMMER\u6216DIAMOND\u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6\u3002<br>--report_orthologs<br>    \u5c06\u7528\u4e8e\u529f\u80fd\u6ce8\u91ca\u7684ortholog\u4fe1\u606f\u8f93\u51fa\u5230\u4e00\u4e2a\u5355\u72ec\u7684\u6587\u4ef6\u4e2d\u3002<br><br><strong>\u6bd4\u5bf9\u53c2\u6570\uff1a<\/strong><br>-m &lt;string>    default: hmmer<br>    \u8bbe\u7f6e\u6bd4\u5bf9\u7b97\u6cd5\u3002\u53ef\u4ee5\u9009\u62e9\u7684\u503c\u4e3ahmmer\u548cdiamond\u3002<br>--hmm_maxhits &lt;int>    default: 1<br>    \u8bbe\u7f6eHMMER\u7b97\u6cd5\u5f97\u5230\u7684hit\u7ed3\u679c\u6570\u91cf\u3002<br>--hmm_evalue &lt;float>    default: 0.001<br>    \u8bbe\u7f6eHMMER\u7b97\u6cd5\u7684evalue\u9608\u503c\u3002<br>--hmm_score &lt;int>    default: 20<br>    \u8bbe\u7f6eHMMER\u7b97\u6cd5\u7684score\u9608\u503c\u3002<br>--hmm_maxseqlen &lt;int>    default: 5000<br>    \u5ffd\u7565\u957f\u5ea6\u8d85\u8fc7\u6b64\u9608\u503c\u7684query\u5e8f\u5217\u3002<br>--hmm_qcov &lt;float>    default: disabled<br>    \u8bbe\u7f6eHMMER\u7b97\u6cd5\u4e2dquery\u5e8f\u5217\u7684\u6700\u5c0f\u8986\u76d6\u7387\u9608\u503c\u3002<br>--dmnd_db &lt;string><br>    \u5f53\u4f7f\u7528DIAMOND\u7b97\u6cd5\u65f6\uff0c\u8bbe\u7f6eDIAMOND\u6570\u636e\u5e93\u8def\u5f84\u3002<br>--matrix &lt;string>    default: BLOSUM62<br>    \u8bbe\u7f6eDIAMOND\u7b97\u6cd5\u7684\u8ba1\u5206\u4e3e\u8bc1\u3002<br>--gapopen &lt;int><br>    \u8bbe\u7f6eDIAMOND\u7b97\u6cd5\u4e2d\u6253\u5f00Gap\u7f5a\u5206\u503c\u3002<br>--gapextend &lt;int><br>    \u8bbe\u7f6eDIAMOND\u7b97\u6cd5\u4e2d\u5ef6\u957fGap\u7f5a\u5206\u503c\u3002<br>--seed_ortholog_evalue &lt;float>    default: 0.001<br>    \u8fdb\u884cseed ortholog\u9274\u5b9a\u65f6\uff0c\u8bbe\u5b9a\u7684evalue\u9608\u503c\u3002<br>--seed_ortholog_score &lt;int>    default: 60<br>    \u8fdb\u884cseed ortholog\u9274\u5b9a\u65f6\uff0c\u8bbe\u5b9a\u7684score\u9608\u503c\u3002 <br><br><strong>\u529f\u80fd\u6ce8\u91ca\u53c2\u6570\uff1a<br><\/strong>--tax_scope &lt;string><br>    \u4ec5\u4f7f\u7528\u6307\u5b9a\u7269\u79cd\u7c7b\u4e0b\u7684\u540c\u6e90\u57fa\u56e0\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\u662f\u5206\u522b\u5bf9\u6bcf\u6761query\u5e8f\u5217\u8fdb\u884c\u81ea\u52a8\u8c03\u8282\u3002<br>--target_orthologs &lt;string><br>    \u8fdb\u884c\u529f\u80fd\u6ce8\u91ca\u65f6\uff0c\u8bbe\u7f6e\u9009\u62e9\u4ec0\u4e48\u7c7b\u578b\u7684\u540c\u6e90\u57fa\u56e0\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca\u3002\u53ef\u4ee5\u9009\u62e9\u7684\u503c\u6709\uff1aone2one,many2one,one2many,many2many,all\u3002<br>--go_evidence &lt;string><br>    \u8bbe\u7f6e\u4f7f\u7528\u4ec0\u4e48\u7c7b\u578b\u7684GO terms\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca\u3002\u53ef\u4ee5\u8bbe\u7f6e\u7684\u503c\u6709\uff1aexperimental\uff0c\u4ec5\u4f7f\u7528\u6e90\u81ea\u5b9e\u9a8c\u8bc1\u636e\u652f\u6301\u7684GO terms\uff1bnon-electronic\uff0c\u4ec5\u4f7f\u7528\u975e\u7535\u5b50\u8ba1\u7b97\u5f52\u7eb3\u7684Go terms\u3002<br><br><strong>\u6027\u80fd\u53c2\u6570\uff1a<br><\/strong>--cpu &lt;int><br>    \u8bbe\u7f6e\u7a0b\u5e8f\u4f7f\u7528\u7684CPU\u7ebf\u7a0b\u6570\u3002<br>--usemem<br>    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u80fd\u5c06HMM\u6570\u636e\u5e93\u8bfb\u53d6\u5230\u5185\u5b58\u4e2d\uff0c\u589e\u52a0\u8ba1\u7b97\u6027\u80fd\u3002\u5728\u7a0b\u5e8f\u8fd0\u884c\u7ed3\u675f\u540e\uff0c\u91ca\u653e\u5185\u5b58\u3002<br>--servermode<br>    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u4f1a\u81ea\u52a8\u6dfb\u52a0--usemem\u53c2\u6570\uff0c\u5c06HMM\u6570\u636e\u5e93\u8bfb\u53d6\u5230\u5185\u5b58\u4e2d\uff0c\u5e76\u4e00\u76f4\u5c06HMM\u6570\u636e\u5e93\u7ef4\u6301\u5230\u5185\u5b58\u4e2d\uff0c\u5e76\u63d0\u4f9b\u6570\u636e\u5e93\u670d\u52a1\uff0c\u76f4\u5230\u5f3a\u884c\u7ed3\u675f\u7a0b\u5e8f\u3002<\/pre>\n\n\n\n<h2>5. eggNOG\u7ed3\u679c\u89e3\u8bfb\u548c\u5206\u7c7b\u56fe\u7ed8\u5236<\/h2>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. EggNOG\u6570\u636e\u5e93\u7b80\u4ecb eggNOG ( Evolutionary Gen &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2804\">\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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2804"}],"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=2804"}],"version-history":[{"count":29,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2804\/revisions"}],"predecessor-version":[{"id":2856,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2804\/revisions\/2856"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2804"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2804"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2804"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}