{"id":2177,"date":"2014-06-30T11:48:52","date_gmt":"2014-06-30T03:48:52","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2177"},"modified":"2014-07-02T10:16:57","modified_gmt":"2014-07-02T02:16:57","slug":"trnascan-se-%e7%9a%84%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2177","title":{"rendered":"tRNAscan-SE \u7684\u4f7f\u7528"},"content":{"rendered":"

1. tRNAscan-SE \u7b80\u4ecb<\/h1>\n

tRNAscan-SE \u80fd\u5728\u57fa\u56e0\u7ec4\u6c34\u5e73\u4e0a\u8fdb\u884c tRNA \u626b\u63cf\u3002\u8be5\u8f6f\u4ef6\u5b9e\u9645\u4e0a\u662f\u4e00\u4e2a perl \u811a\u672c\uff0c\u6574\u5408\u4e86 tRNAscan\u3001 EufindRNA \u548c Cove \u8fd9 3 \u4e2a\u72ec\u7acb\u7684 tRNA \u68c0\u6d4b\u8f6f\u4ef6\u3002tRNAscan-SE \u9996\u5148\u8c03\u7528 tRNAscan \u548c EufindRNA \u9274\u5b9a\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e2d\u7684 tRNA \u533a\u57df\uff0c\u7136\u540e\u8c03\u7528 Cove \u8fdb\u884c\u9a8c\u8bc1\u3002\u8fd9\u6837\u65e2\u4fdd\u8bc1\u4e86\u524d\u8005\u7684 sensitivities\uff0c \u53c8\u4fdd\u8bc1\u4e86\u540e\u8005\u8f83\u4f4e\u7684\u5047\u9633\u6027\u6982\u7387\uff0c\u540c\u65f6\u5728\u641c\u7d22\u901f\u5ea6\u4e0a\u63d0\u5347\u4e86\u5f88\u591a\u3002
\n\u6709\u5173 tRNAscan-SE \u7684\u8be6\u7ec6\u8bf4\u660e\uff0c\u53c2\u8003\u5176\u672c\u5730\u5316\u8f6f\u4ef6\u5305\u4e2d\u7684 man \u6587\u6863\u3002
\ntRNAscan-SE \u7684\u7f51\u9875\u7248\uff1ahttp:\/\/lowelab.ucsc.edu\/tRNAscan-SE\/\u3002\u4f46\u4e00\u6b21\u6700\u591a\u53ea\u80fd\u8fdb\u884c 5M bp \u5e8f\u5217\u7684 tRNA \u9884\u6d4b\u3002<\/p>\n

2. tRNAscan-SE \u672c\u5730\u5b89\u88c5<\/h1>\n
\r\n$ wget http:\/\/lowelab.ucsc.edu\/software\/tRNAscan-SE.tar.gz\r\n$ tar zxf tRNAscan-SE.tar.gz\r\n$ cd tRNAscan-SE-1.3.1\r\n$ perl -p -i -e 's#\\$\\(HOME\\)#\/opt\/biosoft\/tRNAscan-SE-1.3.1#' Makefile\r\n$ make && make install\r\n$ make testrun\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/tRNAscan-SE-1.3.1\/bin\/' >> ~\/.bashrc\r\n$ echo 'PERL5LIB=$PERL5LIB:\/opt\/biosoft\/tRNAscan-SE-1.3.1\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n
3. tRNAscan-SE \u7684\u4f7f\u7528<\/h1>\n
\u5e38\u7528\u4f8b\u5b50\u4e0e\u4e3b\u8981\u53c2\u6570\uff1a<\/p>\n
\r\n$ tRNAscan-SE -o tRNA.out -f rRNA.ss -m tRNA.stats genome.fasta\r\n\r\n-A \u9002\u5408\u4e8e\u53e4\u7ec6\u83cc\u3002\u8be5\u53c2\u6570\u9009\u62e9\u4e86\u53e4\u7ec6\u83cc\u7279\u5f02\u6027\u7684covariance model(cm)\uff0c\u540c\u65f6\u7a0d\u5fae\u653e\u5bbd\u4e86 EufindtRNA \u7684 cutoffs\u3002\r\n-B \u9002\u5408\u4e8e\u7ec6\u83cc\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u4e0d\u9009\u62e9\uff0c-A -B -G \u6216 -O \u53c2\u6570\uff0c\u5219\u9002\u5408\u4e8e\u771f\u6838\u751f\u7269\u3002\r\n-G \u9002\u5408\u4e8e\u53e4\u7ec6\u83cc\uff0c\u7ec6\u83cc\u548c\u771f\u6838\u751f\u7269\u7684\u6df7\u5408\u5e8f\u5217\u3002\u8be5\u53c2\u6570\u4f7f\u7528 general tRNA covariance model\u3002\r\n-O \u9002\u5408\u4e8e\u7ebf\u7c92\u4f53\u548c\u53f6\u7eff\u4f53\u3002\u9009\u62e9\u8be5\u53c2\u6570\uff0c\u5219\u4ec5\u4f7f\u7528 Cove \u8fdb\u884c\u5206\u6790\uff0c\u641c\u7d22\u901f\u5ea6\u4f1a\u5f88\u6162\uff0c\u540c\u65f6\u4e5f\u4e0d\u80fd\u7ed9\u51fa pseudogenes \u68c0\u6d4b\u3002\r\n-i \u4f7f\u7528 Infernal cm analysis only\u3002\u8be5\u53c2\u6570\u8bbe\u7f6e\u540e\uff0c\u9700\u8981 cmsearch \u547d\u4ee4\uff0c\u4f46\u662f tRNAscan-SE \u8f6f\u4ef6\u5305\u4e2d\u8c8c\u4f3c\u6ca1\u6709\u8be5\u7a0b\u5e8f\uff0c\u6700\u7ec8\u65e0\u6cd5\u8fd0\u884c\u3002\r\n-C \u4ec5\u4f7f\u7528 Cove \u8fdb\u884c tRNA \u5206\u6790\u3002\u867d\u7136\u4ece\u4e00\u5b9a\u7a0b\u5ea6\u4e0a\u63d0\u9ad8\u4e86\u51c6\u786e\u6027\uff0c\u4f46\u662f\u4f1a\u6781\u6162\uff0c\u5f53\u7136\u4e0d\u5efa\u8bae\u4e86\u3002\r\n-o <file> \u5c06\u7ed3\u679c\u4fdd\u5b58\u5230\u6587\u4ef6\u3002\r\n-f <file> \u5c06 tRNA \u7684\u4e8c\u7ea7\u7ed3\u6784\u7ed3\u679c\u4fdd\u5b58\u5230\u6587\u4ef6\r\n-m <file> \u5c06\u7edf\u8ba1\u7ed3\u679c\u4fdd\u5b58\u5230\u6587\u4ef6\u3002\r\n<\/pre>\n
4. tRNAscan-SE \u7684\u7ed3\u679c\u8bf4\u660e<\/h1>\n
\u5728\u771f\u6838\u751f\u7269\u4e2d\uff0ctRNA \u7531 RNA \u805a\u5408\u9176III \u5728\u6838\u5185\u8f6c\u5f55\u751f\u6210 pre-tRNA, \u518d\u8fdb\u884c\u52a0\u5de5\u751f\u6210\u6709\u529f\u80fd\u7684 tRNA \u5206\u5b50\uff08\u7279\u522b\u662f\u4e00\u4e9b tRNA \u5e8f\u5217\u8fd8\u542b\u6709\u5185\u542b\u5b50\uff09\u3002\u82e5 tRNA \u5b58\u5728\u5185\u542b\u5b50\uff0c\u5219\u7ed3\u679c\u6587\u4ef6\u4e2d\u7b2c 7 8 \u5217\u4f1a\u7ed9\u51fa\u5185\u542b\u5b50\u533a\u95f4\uff0c\u5426\u5219\u5176\u503c\u4e3a 0 \u3002
\ntRNAscan-SE \u7684\u7ed3\u679c\u4e2d, \u5982\u679c begin \u6bd4 end \u7684\u503c\u5927\uff0c\u5219\u8868\u793a tRNA \u5728\u8d1f\u4e49\u94fe\u4e0a\u3002
\n\u6709\u4e9b\u7ed3\u679c\u4e2d\u7b2c 5 \u5217\u4e3a pseudogene\uff0c \u8fd9\u8868\u793a\u5176\u4e00\u7ea7\u6216\u4e8c\u7ea7\u7ed3\u6784\u6bd4\u8f83\u5dee\u3002
\n\u6700\u540e\u4e00\u5217\u662f Cove Score\uff0c\u8be5\u5206\u503c\u6700\u4f4e\u9608\u503c\u4e3a 20 \u3002\u8be5\u503c\u662f\u4e00\u4e2a log  ratio\u503c\u3002ratio \u662f\u7b26\u5408 tRNA covariance model\u6982\u7387\u4e0e\u968f\u673a\u5e8f\u5217\u6a21\u578b\u6982\u7387\u7684\u6bd4\u503c\u3002
\n\u5f53\u7136\uff0c\u6700\u540e\u6700\u597d\u662f\u5c06\u8868\u683c\u683c\u5f0f\u7ed3\u679c\u8f6c\u6362\u4e3a GFF3 \u7ed3\u679c\uff0c\u4ee5\u5229\u4e8e\u5728\u57fa\u56e0\u7ec4\u4e0a\u7684\u53ef\u89c6\u5316\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
1. tRNAscan-SE \u7b80\u4ecb tRNAscan-SE \u80fd\u5728\u57fa\u56e0\u7ec4\u6c34\u5e73\u4e0a\u8fdb\u884c … \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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2177"}],"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=2177"}],"version-history":[{"count":5,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2177\/revisions"}],"predecessor-version":[{"id":2184,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2177\/revisions\/2184"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2177"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2177"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2177"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}