{"id":1979,"date":"2013-10-29T23:05:37","date_gmt":"2013-10-29T15:05:37","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=1979"},"modified":"2013-10-29T23:33:10","modified_gmt":"2013-10-29T15:33:10","slug":"rnammer%e7%9a%84%e5%ae%89%e8%a3%85%e5%92%8c%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1979","title":{"rendered":"RNAmmer\u7684\u5b89\u88c5\u548c\u4f7f\u7528"},"content":{"rendered":"<h1>1. RNAmmer\u7b80\u4ecb<\/h1>\n<p>RNAmmer\u662f\u7528\u6765\u9884\u6d4brRNA\u7684\u8f6f\u4ef6\u3002\u5176\u5b98\u7f51\u9875\u5de5\u5177\uff1a<a href=\"http:\/\/www.cbs.dtu.dk\/services\/RNAmmer\/\" target=\"_blank\">RNAmmer 1.2 Server<\/a><\/p>\n<p>\u53c2\u8003\u6587\u732e\uff1a<a href=\"http:\/\/nar.oxfordjournals.org\/content\/35\/9\/3100.full\" target=\"_blank\">Lagesen K, Hallin P, R\u00f8dland E A, et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes[J]. Nucleic acids research, 2007, 35(9): 3100-3108.<\/a><\/p>\n<p>RNAmmer\u7684\u6b63\u5e38\u8fd0\u884c\u9700\u8981\uff1a1. perl\u7684Getopt::Long\u548cXML::Simple\u6a21\u5757\uff1b 2. hmmsearch,\u9700\u8981\u5b89\u88c5hmmer-2.2g\u7248\u672c\uff0c\u4f7f\u7528\u6700\u65b0\u7248\u672c\u4f1a\u51fa\u9519\u3002<\/p>\n<h1>2. RNAmmer\u7684\u5b89\u88c5\u548c\u8fd0\u884c<\/h1>\n<pre>\r\n\u4e0b\u8f7d\u5e76\u5b89\u88c5hmmer-2.2g\r\n$ wget ftp:\/\/selab.janelia.org\/pub\/software\/hmmer\/2.2g\/hmmer-2.2g.tar.gz\r\n$ tar zxf hmmer-2.2g.tar.gz\r\n$ cd hmmer-2.2g\r\n$ .\/configure --prefix=\/opt\/biosoft\/hmmer-2.2g\r\n$ mkdir -p \/opt\/biosoft\/hmmer-2.2g\/man\/man1\/ \/opt\/biosoft\/hmmer-2.2g\/bin\r\n$ make; make install\r\n\r\n\u5b89\u88c5RNAmmer\uff0c\u8be5\u8f6f\u4ef6\u9700\u8981\u4f7f\u7528edu\u90ae\u7bb1\u53bb\u7533\u8bf7\u3002\r\n$ mkdir -p \/opt\/biosoft\/rnammer-1.2\r\n$ tar zxf rnammer-1.2.src.tar.Z -C \/opt\/biosoft\/rnammer-1.2\r\n$ perl -p -i -e 's\/(my \\$INSTALL_PATH).*\/$1 = \\\"\\\/opt\\\/biosoft\\\/rnammer-1.2\\\";\/' \/opt\/biosoft\/rnammer-1.2\/rnammer\r\n$ perl -p -i -e 's\/^(\\s+\\$HMMSEARCH_BINARY).*\/$1 = \\\"\\\/opt\\\/biosoft\\\/hmmer-2.2g\\\/bin\\\/hmmsearch\\\";\/' \/opt\/biosoft\/rnammer-1.2\/rnammer\r\n\r\n\u68c0\u6d4b\u662f\u5426\u6b63\u5e38\u8fd0\u884c\r\n$ \/opt\/biosoft\/rnammer-1.2\/rnammer -S bac -multi -f rRNA.fasta\\\r\n -h rRNA.hmmreport -xml rRNA.xml -gff rRNA.gff2\\\r\n \/opt\/biosoft\/rnammer-1.2\/example\/ecoli.fsa\r\n<\/pre>\n<h1>3. RNAmmer\u7684\u8fd0\u884c\u4e0e\u53c2\u6570<\/h1>\n<p>\u8fd0\u884c\/opt\/biosoft\/rnammer-1.2\/rnammer\u547d\u4ee4\uff0c\u53c2\u8003manual\u6587\u4ef6\/opt\/biosoft\/rnammer-1.2\/man\/rnammer.1, \u8be5\u7a0b\u5e8f\u7684\u8fd0\u884c\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n<pre>\r\nUSAGE:\r\n$ rnammer [options] sequence.fasta\r\n\r\n-S  \u6307\u5b9a\u8f93\u5165\u5e8f\u5217\u7684\u7269\u79cd\u6240\u5c5e\u7684\u754c\uff1a arc bac \u6216 euk\r\n\r\n-gff  \u751f\u6210\u7684gff\u6587\u4ef6\u7ed3\u679c\r\n\r\n-m  \u6240\u9700\u8981\u9884\u6d4b\u7684moleculers\uff1a 'tsu' for 5\/8s rRNA, 'ssu' for 16\/18s rRNA, 'lsu' for 23\/28s rRNA\u3002\u5982\u679c\u5168\u90e8\u8fdb\u884c\u9884\u6d4b\uff0c\u5219\u8be5\u53c2\u6570\u540e\u4e3a 'tsu,ssu,lsu'\u3002\r\n\r\n-multi  \u5e76\u884c\u8fd0\u7b97\uff0c\u9884\u6d4b\u6b63\u53cd\u4e24\u6761\u94fe\u4e0a\u6240\u6709\u7684moleculers\u3002\u6700\u591a\u5e76\u884c\u8fd0\u884c6\u4e2a\u8ba1\u7b97\u3002\u4f7f\u7528\u8be5\u53c2\u6570\uff0c\u5219\u4e0d\u9700\u8981\u4e0a\u4e00\u4e2a\u53c2\u6570\u3002\r\n\r\n-f  \u751f\u6210\u7684rRNA\u7684fasta\u7ed3\u679c\u6587\u4ef6\r\n\r\n-h  \u751f\u6210\u7684hmm\u62a5\u544a\u7ed3\u679c\r\n\r\n-gff  \u751f\u6210\u7684rRNA\u7684gff2\u6587\u4ef6\r\n\r\n-x  \u751f\u6210\u7684xml\u7ed3\u679c\u6587\u4ef6\r\n<\/pre>\n<p>\u5bf9\u771f\u6838\u751f\u7269\u57fa\u56e0\u7ec4\u8fdb\u884crRNA\u9884\u6d4b\u7684\u4e00\u4e2a\u793a\u4f8b\u547d\u4ee4:<\/p>\n<pre>\r\n$ \/opt\/biosoft\/rnammer-1.2\/rnammer -S euk -multi -f rRNA.fasta\\\r\n -h rRNA.hmmreport -xml rRNA.xml -gff rRNA.gff2 genome.fasta\r\n<\/pre>\n<h1>4. RNAmmer\u7684\u7ed3\u679c<\/h1>\n<p>rRNA.fasta\uff0crRNA.gff2\uff0crRNA.hmmreport\uff0crRNA.xml\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. RNAmmer\u7b80\u4ecb RNAmmer\u662f\u7528\u6765\u9884\u6d4brRNA\u7684\u8f6f\u4ef6\u3002\u5176\u5b98\u7f51\u9875\u5de5\u5177\uff1a &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1979\">\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":[3],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1979"}],"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=1979"}],"version-history":[{"count":7,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1979\/revisions"}],"predecessor-version":[{"id":1986,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1979\/revisions\/1986"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1979"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1979"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1979"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}