{"id":2185,"date":"2014-07-03T10:30:43","date_gmt":"2014-07-03T02:30:43","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2185"},"modified":"2014-07-03T10:36:14","modified_gmt":"2014-07-03T02:36:14","slug":"%e4%bd%bf%e7%94%a8-rfam-%e8%bf%9b%e8%a1%8c-ncrna-%e6%b3%a8%e9%87%8a","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2185","title":{"rendered":"\u4f7f\u7528 rfam \u8fdb\u884c ncRNA \u6ce8\u91ca"},"content":{"rendered":"<h1>1. rfam \u7b80\u4ecb<\/h1>\n<p>Rfam \u662f\u4e00\u4e2a\u6570\u636e\u5e93\uff0c\u7528\u4e8e\u9274\u5b9a non-coding RNAs\u3002<br \/>\n\u5176\u5b98\u7f51\uff1a<a href=\"http:\/\/rfam.sanger.ac.uk\" target=\"_blank\">http:\/\/rfam.sanger.ac.uk<\/a>\u3002<br \/>\n\u5176\u53c2\u8003\u6587\u732e\uff1a<a href=\"http:\/\/nar.oxfordjournals.org\/content\/41\/D1\/D226.full\" target=\"_blank\">Rfam 11.0: 10 years of RNA families<\/a>\u3002<\/p>\n<h1>2. rfam \u5b89\u88c5<\/h1>\n<p>\u8bf4\u660e\u6587\u6863\uff1a<a href=\"ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/Rfam\/CURRENT\/rfam_scan\/Expandednotesonrunningrfam_scan.pl.txt\" target=\"_blank\">ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/Rfam\/CURRENT\/rfam_scan\/Expandednotesonrunningrfam_scan.pl.txt<\/a><\/p>\n<h2>2.1 \u4e0b\u8f7d rfam_scan.pl \u8f6f\u4ef6<\/h2>\n<p>\u4e0b\u8f7d\u6700\u65b0\u7248\u672c\u7684 rfam_scan.pl \u8f6f\u4ef6<\/p>\n<pre>\r\n$ mkdir \/opt\/biosoft\/rfam\r\n$ cd \/opt\/biosoft\/rfam\r\n$ wget ftp:\/\/ftp.sanger.ac.uk\/pub\/databases\/Rfam\/CURRENT\/rfam_scan\/rfam_scan.pl\r\n$ chmod 755 rfam_scan.pl\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/rfam' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<h2>2.2 \u5b89\u88c5 infernal<\/h2>\n<p>rfam_scan.pl \u7684\u8fd0\u884c\u9700\u8981 infernal \u8f6f\u4ef6\u3002\u6b64\u5916\u8fd8\u9700\u8981 Perl 5.6 \u53ca\u4ee5\u4e0a\u7248\u672c\uff0cNCBI BLAST \u7a0b\u5e8f \u548c Bioperl\u3002<br \/>\nrfam 11 \u7248\u672c\u7684 rfam_scan.pl \u9700\u8981\u5b89\u88c5 infernal 1.0 (1.1\u7248\u672c\u4f1a\u62a5\u9519)\uff1a<\/p>\n<pre>\r\n$ wget http:\/\/selab.janelia.org\/software\/infernal\/infernal-1.0.2.tar.gz\r\n$ tar zxf infernal-1.0.2.tar.gz\r\n$ cd infernal-1.0.2\r\n$ .\/configure --prefix=\/opt\/biosoft\/infernal-1.0.2 && make && make install\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/infernal-1.0.2\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<h2>2.3 \u4e0b\u8f7d\u5e76\u5b89\u88c5 rfam \u7684 blast \u548c cm \u6570\u636e\u5e93<\/h2>\n<p>blast \u6570\u636e\u5e93\u5305\u542b\u4e86\u6240\u6709 rfam \u5bb6\u65cf\u7684\u6838\u9178\u5e8f\u5217\u3002\u5e76\u4e14\u8fd9\u4e9b\u5e8f\u5217\u8fdb\u884c\u4ee5 90% \u7684\u4e00\u81f4\u6027\u8fdb\u884c\u4e86\u53bb\u5197\u4f59\u5904\u7406\u3002<br \/>\ncm \u6570\u636e\u5e93\u5305\u542b\u4e86\u6240\u6709\u7684 rfam \u5bb6\u65cf\u7684 covariance models\u3002<br \/>\nrfam 11 \u7248\u672c\u4e2d\u5305\u542b\u4e86 383,004 \u6761\u5e8f\u5217\u548c 2,208 \u4e2a cms(\u5373 2,208 \u4e2a rfam \u5bb6\u65cf)\u3002<\/p>\n<pre>\r\n$ wget ftp:\/\/ftp.sanger.ac.uk\/pub\/databases\/Rfam\/CURRENT\/Rfam.fasta.gz\r\n$ gzip -d Rfam.fasta.gz\r\n$ formatdb -i Rfam.fasta -p F\r\n$ wget ftp:\/\/ftp.sanger.ac.uk\/pub\/databases\/Rfam\/CURRENT\/Rfam.cm.gz\r\n$ gzip -d Rfam.cm.gz\r\n<\/pre>\n<h3>3. \u4f7f\u7528 rfam<\/h3>\n<p>\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$\u3000rfam_scan.pl -blastdb \/opt\/biosoft\/rfam\/Rfam.fasta \/opt\/biosoft\/rfam\/Rfam.cm genome.fasta -o rfam.gff3\r\n<\/pre>\n<p>\u4e0a\u8ff0\u4f8b\u5b50\u4e2d\uff0c\u8f6f\u4ef6\u5c06\u8c03\u7528 blast \u5c06 query \u5e8f\u5217\u6bd4\u5bf9\u5230 Rfam.fasta \u7684 blast \u6570\u636e\u5e93\u4e2d\uff0c\u53bb\u5bfb\u627e\u76f8\u5e94\u7684 ncRNA \u7684\u76f8\u4f3c\u5e8f\u5217\uff0c\u4f7f\u7528\u7684 blast evalue \u7684\u9608\u503c\u662f 0.01 \u3002 \u7136\u540e\u5c06 blast \u7684\u7ed3\u679c\u518d\u8c03\u7528 cmsearch \u4f7f\u7528 Rfam.cm \u8fdb\u884c\u9a8c\u8bc1\uff0c\u51cf\u5c11\u5047\u9633\u6027\u6982\u7387\u3002\u5982\u679c\u4e0d\u4f7f\u7528 blast\uff0c\u4ec5\u4f7f\u7528 cmsearch \u5219\u901f\u5ea6\u6781\u6162\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. rfam \u7b80\u4ecb Rfam \u662f\u4e00\u4e2a\u6570\u636e\u5e93\uff0c\u7528\u4e8e\u9274\u5b9a non-coding R &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2185\">\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\/2185"}],"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=2185"}],"version-history":[{"count":3,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2185\/revisions"}],"predecessor-version":[{"id":2189,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2185\/revisions\/2189"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2185"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2185"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2185"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}