{"id":650,"date":"2013-03-13T16:11:23","date_gmt":"2013-03-13T08:11:23","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=650"},"modified":"2013-03-15T09:15:45","modified_gmt":"2013-03-15T01:15:45","slug":"interproscan","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=650","title":{"rendered":"InterProScan\u7684\u4e09\u79cd\u4f7f\u7528\u65b9\u6cd5"},"content":{"rendered":"

Interproscan,\u901a\u8fc7\u86cb\u767d\u8d28\u7ed3\u6784\u57df\u548c\u529f\u80fd\u4f4d\u70b9\u6570\u636e\u5e93\u9884\u6d4b\u86cb\u767d\u8d28\u529f\u80fd\u3002\u662fEBI\u5f00\u53d1\u7684\u4e00\u4e2a\u96c6\u6210\u4e86\u86cb\u767d\u8d28\u5bb6\u65cf\u3001\u7ed3\u6784\u57df\u548c\u529f\u80fd\u4f4d\u70b9\u7684\u975e\u5197\u4f59\u6570\u636e\u5e93\u3002Interproscan\u6574\u5408\u4e86\u4e00\u4e9b\u4f7f\u7528\u6700\u666e\u53ca\u7684\u4e00\u4e9b\u6570\u636e\u5e93\uff0c\u5e76\u5e94\u7528\u4e8e\u529f\u80fd\u672a\u77e5\u7684\u86cb\u767d\u8fdb\u884cInterpro\u6ce8\u91ca\u548cGO\u6ce8\u91ca\u3002
\n\u4ee5\u4e0b\u4ecb\u7ecd3\u4e2dinterpro\u6ce8\u91ca\u7684\u65b9\u6cd5\uff1a<\/p>\n

\u4e00\u3001\u7f51\u9875\u7248\u7684Interpro\u6ce8\u91ca<\/h1>\n

\u6253\u5f00InterProScan\u7684\u5b98\u7f51\u5730\u5740\uff1ahttp:\/\/www.ebi.ac.uk\/Tools\/pfa\/iprscan\/<\/a>\u3002\u5c06\u5e8f\u5217\u7c98\u8d34\u5230\u8f93\u5165\u6846\u4e2d\u8fdb\u884cInterpro\u6ce8\u91ca\u3002<\/p>\n

\u4f18\u70b9\uff1a\u4f7f\u7528\u7f51\u9875\u7248\uff0c\u65b9\u4fbf\u5feb\u6377\uff1b\u4e0d\u6d88\u8017\u672c\u5730\u8ba1\u7b97\u8d44\u6e90\u3002\r\n\u7f3a\u70b9\uff1a\u8f93\u5165\u5fc5\u987b\u4e3a\u86cb\u767d\u8d28\u5e8f\u5217\uff1b\u4e00\u6b21\u53ea\u80fd\u6bd4\u5bf9\u6761\u86cb\u767d\u8d28\u5e8f\u5217\u3002<\/pre>\n
\u4e8c\u3001\u4f7f\u7528EBI\u63d0\u4f9b\u7684perl\u7a0b\u5e8f\u8fdb\u884c\u8fdc\u7a0b\u6bd4\u5bf9<\/h1>\n
\u7a0b\u5e8f\u4e0b\u8f7d\u7f51\u9875\u5730\u5740\uff1ahttp:\/\/www.ebi.ac.uk\/Tools\/webservices\/services\/pfa\/iprscan_rest<\/a>\u3002
\n\u5176\u5b9e\uff0c\u9664\u4e86perl\u7a0b\u5e8f\uff0cPython\u548cRuby\u4e5f\u5404\u6709\u4e00\u652f\u7a0b\u5e8f\u3002\u5206\u522b\u662f\uff1a
\niprscan_lwp.pl<\/a> ; iprscan_urllib2.py<\/a> ; iprscan_net_http.rb<\/a>\u3002<\/p>\n
\u4f18\u70b9\uff1a\u4e0d\u6d88\u8017\u672c\u5730\u8ba1\u7b97\u8d44\u6e90\uff1b\u53ef\u4ee5\u81ea\u5df1\u7f16\u5199\u811a\u672c\u6765\u5927\u6279\u91cf\u6bd4\u5bf9\u672c\u5730\u7684protein\u5e8f\u5217\u5230EBI\u7684\r\ninterpro\u670d\u52a1\u5668\uff0c\u83b7\u5f97\u5f97interpro\u6ce8\u91ca\u3002\r\n\u7f3a\u70b9\uff1a\u6bd4\u5bf9\u7ed3\u679c\u4e3axml\u683c\u5f0f\uff0c\u666e\u901a\u79d1\u7814\u4eba\u5458\u73a9\u4e0d\u6765\u3002<\/pre>\n
\u4e09\u3001\u672c\u5730\u5316\u7684InterProScan\u6ce8\u91ca<\/h1>\n
3.1 \u672c\u5730\u5316\u7684InterProScan\u5b89\u88c5\u4e0e\u914d\u7f6e<\/h2>\n
3.1.1 \u4eceftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/interpro\/iprscan<\/a>\u4e0b\u8f7d\u4ee5\u4e0b5\u4e2a\u6587\u4ef6\uff1a<\/p>\n
RELEASE\/latest\/iprscan_v4.8.tar.gz\r\nBIN\/4.x\/iprscan_bin4.x_[PLATFORM].tar.gz \r\nDATA\/iprscan_DATA_[LATESTDATAVERSION].tar.gz\r\nDATA\/iprscan_PTHR_DATA_[LATESTDATAVERSION].tar.gz\r\nDATA\/iprscan_MATCH_DATA_[LATESTDATAVERSION].tar.gz<\/pre>\n
3.1.2 \u5c065\u4e2a\u6587\u4ef6\u89e3\u538b\u5230\u4e00\u4e2a\u6587\u4ef6\u5939\u4e2d\uff0c\u7136\u540e\u8fd0\u884c\u5176\u4e2d\u7684\u6587\u4ef6Config.pl\uff0c\u6765\u5bf9InterProScan\u8fdb\u884c\u914d\u7f6e\u3002
\n3.1.3 \u914d\u7f6e\u7684\u8fc7\u7a0b\u4e2d\uff0c\u82e5\u9009\u62e9\u8fdb\u884c\u672c\u5730web\u914d\u7f6e\uff0c\u5219\u4fee\u6539\u672c\u5730www\u670d\u52a1\u7684\u914d\u7f6e\u6587\u4ef6\uff0c\u4ee5\u80fd\u8fdb\u884c\u672c\u5730\u5316\u7f51\u9875\u7248\u7684\u8fd0\u884c\u3002<\/p>\n
3.2 \u672c\u5730\u5316InterProScan\u7684\u4f7f\u7528\u3002<\/h2>\n
3.2.1 \u547d\u4ee4\u884c\u8fd0\u884ciprscan\u7684\u65b9\u6cd5\uff1a<\/p>\n
$ bin\/iprscan -cli -iprlookup -goterms -format xml -i test.fasta -o test.out<\/pre>\n
3.2.2 iprscan\u7684\u53c2\u6570\u8bf4\u660e\uff1a<\/p>\n
-cli         \u8bbe\u5b9a\u7a0b\u5e8f\u5728unix\u547d\u4ee4\u4e0b\u8fd0\u884c\uff0c\u5982\u679c\u4e0d\u8bbe\u6b64\u53c2\u6570\uff0c\u7a0b\u5e8f\u4f1a\u88ab\u5f53\u4f5cCGI\u7a0b\u5e8f\u8fd0\u884c\u3002\r\n-iprlookup   \u7ed3\u679c\u91cc\u663e\u793a\u76f8\u5e94\u7684interpro\u6ce8\u91ca\u4fe1\u606f\u3002\r\n-goterms     \u7ed3\u679c\u91cc\u663e\u793a\u76f8\u5e94\u7684GO\u6ce8\u91ca\u4fe1\u606f\uff0c\u4f46\u524d\u9762\u8981\u52a0\u4e0a-iprlookup\u53c2\u6570\u3002\r\n-format      \u8f93\u51fa\u7ed3\u679c\u7684\u683c\u5f0f\uff0c\u6709raw, xml, txt, html(default), ebixml\r\n(EBI header on top of xml) gff\u3002\r\n-appl  \u6570\u636e\u5e93\u548c\u626b\u63cf\u65b9\u6cd5\u7684\u7684\u9009\u62e9\u3002\u65e0\u6b64\u53c2\u6570\u8868\u793a\u9ed8\u8ba4\u9009\u62e9\u5168\u90e8\u6570\u636e\u5e93\uff08\u914d\u7f6eInterpro\r\nscan\u65f6\u5019\u8bbe\u7f6e\u7684\u6570\u636e\u5e93\uff09\u3002\u9009\u62e9\u591a\u4e2a\u6570\u636e\u5e93\u5219\u9700\u8be5\u53c2\u6570\u591a\u6b21\u3002\u672c\u5730\u8fd0\u884cInterproscan\u76f8\r\n\u6bd4\u5b98\u7f51\u8fd0\u884c\uff0c\u6709\u4e24\u4e2a\u6570\u636e\u5e93\u4e0d\u80fd\u9009\u62e9\u4e3a\uff1atmhmm \u548c signalp\u3002\u8fd9\u4e24\u4e2a\u6570\u636e\u5e93\u7684\u9009\u62e9\u9700\u8981\r\ncommercial license\u3002\r\n-i           \u8f93\u5165\u6587\u4ef6\uff0cInterProScan\u652f\u6301\u8f93\u5165\u86cb\u767d\u8d28\u5e8f\u5217\u548c\u6838\u9178\u5e8f\u5217\uff0c\u5982\u679c\u8f93\u5165\u6838\r\n\u9178\u7cfb\u5217\uff0c\u7a0b\u5e8f\u4f1a\u5c06\u5176\u7ffb\u8bd1\u6210\u86cb\u767d\u8d28\u5e8f\u5217\uff0c\u4f60\u53ef\u4ee5\u6307\u5b9a\u7ffb\u8bd1\u7528\u5230\u7684\u5bc6\u7801\u8868\uff0c\u7528\u4e0b\u9762\u7684-trtable\r\n\u53c2\u6570\uff0c\u5e8f\u5217\u683c\u5f0f\u53ef\u4ee5\u662fraw\uff0cFasta\u6216\u8005EMBL\u3002\r\n-o           \u7ed3\u679c\u8f93\u51fa\u6587\u4ef6\uff0c\u5982\u679c\u4e0d\u9009\u62e9\u6b64\u53c2\u6570\uff0c\u7ed3\u679c\u5c06\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\uff0c\u8f93\u51fa\u683c\u5f0f\u53ef\u4ee5\r\n\u7528\u4e0b\u9762\u7684-format\u53c2\u6570\u8bbe\u5b9a\u3002\r\n-trtable   \u9009\u62e9\u6838\u9178\u7ffb\u8bd1\u86cb\u767d\u8d28\u7684\u5bc6\u7801\u8868\uff0c\u540c\u65f6\u53ef\u4ee5\u8bbe\u5b9a-trlen \u53c2\u6570\u6765\u63a7\u5236\u6838\u9178\u7ffb\u8bd1\r\n\u7684\u8f6c\u5f55\u5b50\u957f\u5ea6\u3002\r\n-nocrc       \u4e0d\u5bf9\u8f93\u5165\u86cb\u767d\u8d28\u5e8f\u5217\u8fdb\u884ccrc64\u5339\u914d\u3002\u4e0d\u52a0\u6b64\u53c2\u6570\uff0c\u5219\u9ed8\u8ba4\u662f\u4f1a\u5bf9\u86cb\u767d\u8d28\r\n\u5e8f\u5217\u5f00\u542f\u4e86crc64\u5339\u914d\u3002Interpro\u6570\u636e\u5e93(memember database)\u5df2\u7ecf\u5305\u542b\u4e86\u5927\u91cf\u5e8f\u5217\r\n\u641c\u7d22\u7684\u7ed3\u679c\uff0c\u5c31\u662f\u5982\u679c\u4f60\u7684\u86cb\u767d\u5e8f\u5217\u5df2\u7ecf\u5305\u542b\u5728interpro\u7684\u6570\u636e\u5e93\u91cc\u9762\uff0ciprscan\u4f1a\u76f4\u63a5\r\n\u7ed9\u51fa\u641c\u7d22\u7ed3\u679c\uff0c\u65e0\u9700\u8fdb\u884c\u672c\u5730\u8fd0\u7b97\u3002interpro\u6570\u636e\u5e93\u4e0d\u5305\u62ectmhmm, coil\u548csignalp\uff0c\r\n\u6240\u4ee5crc64\u5339\u914d\u4e0d\u5230\u8fd93\u4e2a\u6570\u636e\u5e93\u3002\u4e00\u822c\u60c5\u51b5\u4e0b\uff0c\u7531\u4e8ecommercial licese\u800c\u65e0\u6cd5\u4f7f\u7528\r\ntmhmm\u548csignalp\u6570\u636e\u5e93\uff0ccoil\u6570\u636e\u5e93\u4e5f\u4e0d\u4f1a\u4f7f\u7528\u3002\u6545\u4e0d\u4f7f\u7528\u6b64\u53c2\u6570\uff0c\u52a0\u5feb\u7a0b\u5e8f\u8fd0\u884c\u901f\u5ea6\u3002\r\n-seqtype  \u00a0 \u00a0\u8f93\u5165\u7684\u5e8f\u5217\u7c7b\u578b\uff0c\u86cb\u767d\u8d28\u5e8f\u5217\uff08-seqtype p\uff09\uff08defult\uff09\u6216\u8005\uff08-se\r\nqtype n\uff09\u3002\r\n-email    \u00a0 \u00a0\u8bbe\u5b9a\u4e00\u4e2aEmail\u5730\u5740\uff0c\u7a0b\u5e8f\u8fd0\u884c\u5b8c\u6bd5\u5411\u4fe1\u7bb1\u53d1\u9001\u90ae\u4ef6\u901a\u77e5\u5206\u6790\u5b8c\u6bd5\u3002\r\n-verbose     \u7a0b\u5e8f\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u663e\u793a\u8fd0\u884c\u7684\u72b6\u6001\u3002\r\n-help        \u663e\u793a\u5e2e\u52a9\u4fe1\u606f\u3002<\/pre>\n
3.2.3 InterProScan\u5176\u5b83\u9644\u5e26\u7684\u91cd\u8981\u7a0b\u5e8f<\/p>\n
meter.pl     reports the progress of a job.\u6709\u767e\u5206\u4e4b\u51e0\u7684chunk\u5df2\u7ecf\u8fd0\u884c\u5b8c\u6bd5\u3002\r\nconverter.pl \u5c06raw\u7684\u683c\u5f0f\u8f6c\u6362\u6210\u5176\u5b83\u7684\u683c\u5f0f\uff0c\u6bd4\u5982html,xml\uff0ctxt\u7b49\u683c\u5f0f\u3002\r\niterator.pl  \u8fd0\u7528\u4e8e\u9010\u6761\u53bb\u6ce8\u91ca\u5e8f\u5217<\/pre>\n
3.2.4 \u591a\u7ebf\u7a0b\u8fd0\u884c
\nhmmpfam, hmmscan \u548c hmmsearch \u80fd\u591a\u7ebf\u7a0b\u8fd0\u884c\u3002
\n\u7ecf\u8fc7\u6d4b\u8bd5 PIR superfamily \u548c SUPERFAMILY \u8fd9\u4e24\u4e2a\u6570\u636e\u5e93\u7684\u5e94\u7528\u6bd4\u8f83\u8d39\u65f6\uff0c\u53ef\u4ee5\u8bbe\u7f6econf\u6587\u4ef6\u5939\u4e2d\u7684\u914d\u7f6e\u6587\u4ef6hmmpir.conf\u548csuperfamily.conf\uff0c\u5c06\u5176\u4e2d\u7684cpu_opt\u7684\u503c\u8bbe\u7f6e\u9ad8\u4e00\u4e9b\u3002\u9ed8\u8ba4\u662f1\u3002
\n3.2.5 \u9010\u6761\u5e8f\u5217\u5730\u8fd0\u884c
\nInterProScan\u4e0d\u80fd\u7acb\u9a6c\u7ed9\u51fa\u7ed3\u679c\u6587\u4ef6\u5e76\u76f8\u7ee7\u628a\u7ed3\u679c\u653e\u5165\u5230\u7ed3\u679c\u6587\u4ef6\u4e2d\u3002\u53ef\u4ee5\u91c7\u7528\u9010\u6761\u6bd4\u5bf9\u7684\u65b9\u6cd5\u6765\u5f97\u5230\u6ce8\u91ca\u7ed3\u679c\u3002\u53ef\u4ee5\u91c7\u7528\u5982\u4e0b\u7684\u65b9\u6cd5\u6765\u968f\u65f6\u7ec8\u7ed3\u6389\u7a0b\u5e8f\uff0c\u5e76\u62ff\u5230\u90e8\u5206\u7ed3\u679c\u3002<\/p>\n
$ bin\/iterator.pl -i test.fa -o test.out -c \"bin\/iprscan -cli -i %infile -iprlookup -goterms -format xml\"<\/pre>\n
3.2.6 \u4f18\u7f3a\u70b9<\/p>\n
\u4f18\u70b9\uff1a\u4f7f\u7528\u672c\u5730\u5316\u7684\u6570\u636e\u5e93\uff0c\u5728\u65ad\u7f51\u548c\u8ba1\u7b97\u673a\u8d44\u6e90\u5145\u8db3\u7684\u60c5\u51b5\u4e0b\uff0c\u80fd\u52a0\u5feb\u6ce8\u91ca\u901f\u5ea6\uff1b\u672c\u5730\u5316\u7f51\r\n\u9875\u7248\u80fd\u540c\u65f6\u6bd4\u5bf9\u591a\u6761\u5e8f\u5217\uff1b\u672c\u5730\u5316\u80fd\u5bf9DNA\u5e8f\u5217\u8fdb\u884cinterpro\u6ce8\u91ca\u3002\r\n\u7f3a\u70b9\uff1a\u672c\u5730\u5316\u5b89\u88c5InterProScan\u6bd4\u8f83\u590d\u6742\u8017\u65f6\uff1b\u9700\u8981\u4e0d\u65f6\u66f4\u65b0\u672c\u5730\u6570\u636e\u5e93\uff1b\u672c\u5730\u5316\u8fd0\u884c\u8017\r\n\u8d39\u8ba1\u7b97\u8d44\u6e90\u5927\uff1b<\/pre>\n","protected":false},"excerpt":{"rendered":"
Interproscan,\u901a\u8fc7\u86cb\u767d\u8d28\u7ed3\u6784\u57df\u548c\u529f\u80fd\u4f4d\u70b9\u6570\u636e\u5e93\u9884\u6d4b\u86cb\u767d\u8d28\u529f\u80fd\u3002\u662fEB … \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":[32],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/650"}],"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=650"}],"version-history":[{"count":13,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/650\/revisions"}],"predecessor-version":[{"id":664,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/650\/revisions\/664"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=650"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=650"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=650"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}