{"id":2274,"date":"2015-08-25T16:28:56","date_gmt":"2015-08-25T08:28:56","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2274"},"modified":"2016-03-18T12:52:29","modified_gmt":"2016-03-18T04:52:29","slug":"%e4%bd%bf%e7%94%a8-hmmer-%e8%bf%9b%e8%a1%8c-pfam-%e6%b3%a8%e9%87%8a","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2274","title":{"rendered":"\u4f7f\u7528 HMMER \u8fdb\u884c PFAM \u6ce8\u91ca"},"content":{"rendered":"

1. HMMER \u7b80\u4ecb<\/h1>\n

HMMER \u548c BLAST \u7c7b\u4f3c\uff0c\u4e3b\u8981\u7528\u4e8e\u5e8f\u5217\u6bd4\u5bf9\u3002<\/p>\n

2. HMMER \u4e0e PFAM \u7684\u4e0b\u8f7d\u5b89\u88c5<\/h1>\n
\r\n\u5b89\u88c5 HMMER\r\n$ wget ftp:\/\/selab.janelia.org\/pub\/software\/hmmer3\/3.1b2\/hmmer-3.1b2.tar.gz\r\n$ tar zxf hmmer-3.1b2.tar.gz\r\n$ cd hmmer-3.1b2\r\n$ .\/configure --prefix=\/opt\/biosoft\/hmmer-3.1b2 && make -j 8 && make install\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/hmmer-3.1b2\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n\u4e0b\u8f7d HMMER \u8f6f\u4ef6\u8bf4\u660e\u6587\u6863\r\n$ wget ftp:\/\/selab.janelia.org\/pub\/software\/hmmer3\/3.1b2\/Userguide.pdf -P  \/opt\/biosoft\/hmmer-3.1b2\/\r\n\r\n\u4e0b\u8f7d PFAM \u6570\u636e\u5e93\r\n$ cd \/opt\/biosoft\/hmmer-3.1b2\/\r\n$ wget ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/Pfam\/releases\/Pfam27.0\/Pfam-A.hmm.gz\r\n$ wget ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/Pfam\/releases\/Pfam27.0\/Pfam-B.hmm.gz\r\n$ gzip -d Pfam-A.hmm.gz; gzip -d Pfam-B.hmm.gz\r\n\u5f97\u5230 PFAM \u6570\u636e\u5e93\u7684 HMM \u6587\u4ef6\u3002 HMM \u6587\u4ef6\u662f\u6587\u672c\u6587\u4ef6\uff0c\u9700\u8981\u5c06\u5176\u53d8\u6210\u4e8c\u8fdb\u5236\u683c\u5f0f\uff0c\u4ee5\u52a0\u5feb\u8fd0\u7b97\u901f\u5ea6\uff0c\u540c\u65f6\u8fdb\u884c\u538b\u7f29\uff0c\u5e76\u5efa\u7acb\u6210\u7d22\u5f15\u6570\u636e\u5e93\u3002\r\n$ hmmpress Pfam-A.hmm\r\n$ hmmpress Pfam-B.hmm\r\n<\/pre>\n
3. \u4f7f\u7528 hmmscan \u8fdb\u884c Pfam \u6ce8\u91ca<\/h1>\n
Pfam \u6570\u636e\u5e93\u4e2d\u6bcf\u4e2a\u7f16\u53f7\u4ee3\u8868\u4e00\u4e2a\u86cb\u767d\u8d28\u5bb6\u65cf\u3002Pfam \u5206 A \u548c B \u4e24\u4e2a\u6570\u636e\u5e93\uff0c\u5176\u4e2d A \u6570\u636e\u5e93\u662f\u7ecf\u8fc7\u624b\u5de5\u6821\u6b63\u7684\u9ad8\u8d28\u91cf\u6570\u636e\u5e93\uff0c B \u6570\u636e\u5e93\u867d\u7136\u8d28\u91cf\u4f4e\u4e9b\uff0c\u4f9d\u7136\u53ef\u4ee5\u7528\u6765\u5bfb\u627e\u86cb\u767d\u8d28\u5bb6\u65cf\u7684\u4fdd\u5b88\u4f4d\u70b9\u3002Pfam \u6700\u65b0 v27.0 \u7248\u672c\u7684\u6570\u636e\u5e93\u4e2d\uff0c A \u6570\u636e\u5e93\u5305\u542b 14,836 \u4e2a\u86cb\u767d\u8d28\u5bb6\u65cf\u7f16\u53f7\uff08\u4ee5 PF \u5f00\u5934\uff09\uff1b B \u6570\u636e\u5e93\u5305\u542b 20,000 \u4e2a\u86cb\u767d\u8d28\u5bb6\u65cf\u7f16\u53f7 \uff08\u4ee5 PB \u5f00\u5934\uff09\u3002
\n\u4f7f\u7528 hmmscan \u8fdb\u884c Pfam \u6ce8\u91ca\u793a\u4f8b\uff1a<\/p>\n
\r\n$ \/opt\/biosoft\/hmmer-3.1b2\/bin\/hmmscan -o out.txt --tblout out.tbl --noali -E 1e-5 \/opt\/biosoft\/hmmer-3.1b2\/Pfam-A.hmm file.fasta\r\n\r\n\u751f\u6210\u7ed3\u679c\u6587\u4ef6 out.txt \u548c out.tbl\r\nout.txt \u6587\u4ef6\u4fe1\u606f\u6bd4\u8f83\u5168\u9762\uff0c\u4f46\u662f\u4e0d\u597d\u9605\u8bfb\uff1b\r\nout.tbl \u6587\u4ef6\u5219\u662f\u8868\u683c\u5f62\u5f0f\u7684\u7ed3\u679c\uff0c\u662f\u4e00\u822c\u9700\u8981\u7684\u7ed3\u679c\u3002\r\n<\/pre>\n
hmmscan \u547d\u4ee4\u7684\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n
\r\n$ hmmscan [-options]  \r\n\r\n-h\r\n    \u663e\u793a\u5e2e\u52a9\u4fe1\u606f\r\n-o FILE\r\n    \u5c06\u7ed3\u679c\u8f93\u51fa\u5230\u6307\u5b9a\u7684\u6587\u4ef6\u4e2d\u3002\u9ed8\u8ba4\u662f\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\u3002\r\n--tblout FILE\r\n    \u5c06\u86cb\u767d\u8d28\u5bb6\u65cf\u7684\u7ed3\u679c\u4ee5\u8868\u683c\u5f62\u5f0f\u8f93\u51fa\u5230\u6307\u5b9a\u7684\u6587\u4ef6\u4e2d\u3002\u9ed8\u8ba4\u4e0d\u8f93\u51fa\u8be5\u6587\u4ef6\u3002\r\n--domtblout FILE\r\n    \u5c06\u86cb\u767d\u7ed3\u6784\u57df\u7684\u6bd4\u5bf9\u7ed3\u679c\u4ee5\u8868\u683c\u5f62\u5f0f\u8f93\u51fa\u5230\u6307\u5b9a\u7684\u6587\u4ef6\u4e2d\u3002\u9ed8\u8ba4\u4e0d\u8f93\u51fa\u8be5\u6587\u4ef6\u3002\u8be5\u8868\u683c\u4e2d\u5305\u542bquery\u5e8f\u5217\u8d77\u59cb\u7ed3\u675f\u4f4d\u70b9\u4e0e\u76ee\u6807\u5e8f\u5217\u8d77\u59cb\u7ed3\u675f\u4f4d\u70b9\u7684\u5339\u914d\u4fe1\u606f\u3002\r\n--acc\r\n    \u5728\u8f93\u51fa\u7ed3\u679c\u4e2d\u5305\u542b PF \u7684\u7f16\u53f7\uff0c\u9ed8\u8ba4\u662f\u86cb\u767d\u8d28\u5bb6\u65cf\u7684\u540d\u79f0\u3002\r\n--noali\r\n    \u5728\u8f93\u51fa\u7ed3\u679c\u4e2d\u4e0d\u5305\u542b\u6bd4\u5bf9\u4fe1\u606f\u3002\u8f93\u51fa\u6587\u4ef6\u7684\u5927\u5c0f\u5219\u4f1a\u66f4\u5c0f\u3002\r\n-E FLOAT    default:10.0\r\n    \u8bbe\u5b9a E_value \u9608\u503c\uff0c\u63a8\u8350\u8bbe\u7f6e\u4e3a 1e-5 \u3002\r\n-T FLOAT\r\n    \u8bbe\u5b9a Score \u9608\u503c\u3002\r\n--domE FLOAT    default:10.0\r\n    \u8bbe\u5b9a E_value \u9608\u503c\u3002\u8be5\u53c2\u6570\u548c -E \u53c2\u6570\u7c7b\u4f3c\uff0c\u4e0d\u8fc7\u662f domain \u6bd4\u5bf9\u8bbe\u5b9a\u7684\u503c\u3002\r\n--cpu\r\n    \u591a\u7ebf\u7a0b\u8fd0\u884c\u7684CPU\u3002\u9ed8\u8ba4\u5e94\u8be5\u662f\u5927\u4e8e1\u7684\uff0c\u8868\u793a\u652f\u6301\u591a\u7ebf\u7a0b\u8fd0\u884c\u3002\u4f46\u5176\u5b9e\u4f30\u8ba1\u4e00\u822c\u4e00\u4e2ahmmscan\u7a0b\u5e8f\u5229\u7528150%\u4e2aCPU\u3002\u5e76\u4e14\u82e5\u8fdb\u884c\u5e76\u884c\u5316\u8c03\u7528hmmscan\uff0c\u5f53\u5e76\u884c\u6570\u9ad8\u4e8e4\u7684\u65f6\u5019\uff0c\u4f1a\u62a5\u9519\uff1aFatal exception (source file esl_threads.c, line 129)\u3002\u8fd9\u65f6\uff0c\u8bbe\u7f6e--cpu\u7684\u503c\u4e3a1\u5373\u53ef\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. HMMER \u7b80\u4ecb HMMER \u548c BLAST \u7c7b\u4f3c\uff0c\u4e3b\u8981\u7528\u4e8e\u5e8f\u5217\u6bd4\u5bf9\u3002 2 … \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":[3],"tags":[67],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2274"}],"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=2274"}],"version-history":[{"count":3,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2274\/revisions"}],"predecessor-version":[{"id":2421,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2274\/revisions\/2421"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2274"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2274"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2274"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}