{"id":2162,"date":"2014-06-20T06:36:54","date_gmt":"2014-06-19T22:36:54","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2162"},"modified":"2016-03-15T16:52:19","modified_gmt":"2016-03-15T08:52:19","slug":"genewise-%e7%9a%84%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2162","title":{"rendered":"GENEWISE \u7684\u4f7f\u7528"},"content":{"rendered":"

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

Genewise\u4e3b\u8981\u7528\u4e8e\u5c06\u86cb\u767d\u8d28\u5e8f\u5217\u548cDNA\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\uff0c\u4ece\u800c\u5bf9DNA\u5e8f\u5217\u4e0a\u7684\u7f16\u7801\u533a\u8fdb\u884c\u9884\u6d4b\u3002<\/p>\n

2. GeneWise \u5b89\u88c5<\/h1>\n
\r\n$ wget http:\/\/www.ebi.ac.uk\/~birney\/wise2\/wise2.4.1.tar.gz\r\n$ tar zxf wise2.4.1.tar.gz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/src\r\n\r\n$ yum install *glib*\r\n$ find .\/ -name makefile | xargs sed -i 's\/glib-config\/pkg-config --libs glib-2.0\/'\r\n$ export C_INCLUDE_PATH=\/usr\/include\/glib-2.0\/:\/usr\/lib64\/glib-2.0\/include\/:$C_INCLUDE_PATH\r\n$ perl -p -i -e 's\/getline\/get_line\/g' .\/HMMer2\/sqio.c\r\n$ perl -p -i -e 's\/isnumber\/isdigit\/' models\/phasemodel.c\r\n$ make all\r\n$ export WISECONFIGDIR=\/opt\/biosoft\/wise2.4.1\/wisecfg\/\r\n$ make test\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/wise2.4.1\/src\/bin\/' >> ~\/.bashrc\r\n$ echo 'export WISECONFIGDIR=\/opt\/biosoft\/wise2.4.1\/wisecfg\/' >> ~\/.bashrc \r\n$ source ~\/.bashrc\r\n<\/pre>\n
3. GeneWise\u7684\u4f7f\u7528<\/h1>\n
\u5728GeneWise\u7684\u5b89\u88c5\u76ee\u5f55\u4e0b\uff0c\u6709\u4e00\u4e2awise2.pdf\u6587\u4ef6\uff0c\u9610\u8ff0\u4e86\u8be6\u7ec6\u7684genewise\u7684\u4f7f\u7528\u65b9\u6cd5\u3002\u5176\u8f6f\u4ef6\u6700\u5e38\u7528\u7684\u547d\u4ee4\u662fgenewise\u3002\u8be5\u547d\u4ee4\u7684\u5e38\u7528\u793a\u4f8b\uff1a<\/p>\n
\r\ngenewise protein.fasta dna.fasta -both -gff\r\n\r\n\u7a0b\u5e8f\u8f93\u5165\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u548cDNA\u5e8f\u5217\u5206\u522b\u662f2\u4e2afasta\u6587\u4ef6\u3002\u8fd9\u4e24\u4e2afasta\u6587\u4ef6\u4e2d\u4ec5\u6709\u7b2c\u4e00\u6761\u5e8f\u5217\u662f\u6709\u6548\u7684\uff0cgenewise\u4ec5\u5bf9\u5176\u4e2d\u76842\u4e2a\u7b2c\u4e00\u6761\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\u3002\u4ee5\u4e0a\u793a\u4f8b\u5bf9dna\u5e8f\u5217\u7684\u6b63\u8d1f\u94fe\u90fd\u8fdb\u884ccds\u9884\u6d4b\uff0c\u5e76\u5c06gff\u683c\u5f0f\u7ed3\u679c\u6587\u4ef6\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\u3002\r\n<\/pre>\n
genewise\u7684\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n
\r\n-trev\r\n    \u4ec5\u5bf9\u8d1f\u4e49\u94fe\u8fdb\u884ccds\u9884\u6d4b\u3002\r\n-tfor\r\n    \u4ec5\u5bf9\u6b63\u4e49\u94fe\u8fdb\u884ccds\u9884\u6d4b\u3002\u8be5\u53c2\u6570\u662f\u9ed8\u8ba4\u503c\u3002\r\n-both\r\n    \u5bf9\u8d1f\u94fe\u90fd\u8fdb\u884ccds\u9884\u6d4b\u3002\r\n-genes\r\n    \u7ed9\u51fagene\u7ed3\u6784\u7684\u7ed3\u679c\uff0c\u975e\u5e38\u7b80\u5355\u7684exon\u4fe1\u606f\u7ed3\u679c\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u4ec5\u8f93\u51fa\u9002\u5408\u4eba\u7c7b\u9605\u8bfb\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\r\n-gff\r\n    \u7ed9\u51fagff\u683c\u5f0f\u7684\u7ed3\u679c\u3002\r\n-cdna\r\n    \u7ed9\u51facdna\u5e8f\u5217\u3002\r\n-pep\r\n    \u7ed9\u51facds\u7ffb\u8bd1\u51fa\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u3002\r\n-splice [model\/flat]\r\n    \u4f7f\u7528\u7684split site\u662fmodel\uff08\u9ed8\u8ba4\u503c\uff09\u6216GT\/AG\u3002\r\n-help\r\n    \u7ed9\u51fa\u5e2e\u52a9\u4fe1\u606f\u3002\r\n-version\r\n    \u7ed9\u51fa\u7248\u672c\u4fe1\u606f\u3002\r\n-silent\r\n    \u6807\u51c6\u9519\u8bef\u8f93\u51fa\u4e0d\u8f93\u51famessages\u4fe1\u606f\u3002\r\n-quiet\r\n    \u6807\u51c6\u9519\u8bef\u8f93\u51fa\u4e0d\u8f93\u51fareport\/info\u4fe1\u606f\u3002\r\n<\/pre>\n
genewise\u7684\u8fd0\u884c\u539f\u7406\u7b80\u8ff0\uff1a<\/p>\n
\r\n1. genewise\u7684\u7b97\u6cd5\uff1a21:93\u7b97\u6cd5\u662fgenewise\u7684\u57fa\u7840\u7b97\u6cd5\u3002\u8be5\u7b97\u6cd5\u7b80\u5355\u8bb2\u5c31\u662f Match-Insert-Delete\uff0c\u5728\u86cb\u767d\u8d28\u5e8f\u5217\u548cDNA\u5e8f\u5217\u6bd4\u5bf9\u540e\u80fd\u51c6\u786e\u5212\u5b9aintron\u8fb9\u754c\u3002\u7b97\u6cd5\u5c06intron\u5206\u62105\u90e8\u5206\uff1a5'\u7aefsplice site\u3001\u4e2d\u95f4intron\u4e3b\u4f53\u3001\u5bcc\u542bCT\u533a\u57df\u3001\u8fde\u63a5\u533a\u30013'\u7aefsplice site\u3002\u6839\u636e\u86cb\u767d\u8d28\u5e8f\u5217\u548cDNA\u5e8f\u5217\u7684\u6bd4\u5bf9\u7ed3\u679c\u7b97\u51faIntron\u90e8\u5206\uff0c\u4ece\u800c\u5c06DNA\u5e8f\u5217\u7684CDS\u533a\u5206\u6210\u4e86Match\u3001Insert\u548cDelete 3\u90e8\u5206\uff0c\u518d\u5bf9\u8fd93\u90e8\u5206\u8fdb\u884c\u86cb\u767d\u8d28\u7ffb\u8bd1\u6216\u79fb\u7801\u7ffb\u8bd1\uff0c\u4ece\u800c\u5212\u5b9aintron\u8fb9\u754c\uff0c\u5f97\u5230CDS\u4fe1\u606f\u3002\r\n2. 6:23\u7b97\u6cd5\u5219\u662f2:93\u7b97\u6cd5\u7684\u7b80\u5355\u7248\u672c\uff0c\u4e5f\u662f\u8f6f\u4ef6\u7684\u9ed8\u8ba4\u8bbe\u7f6e\u3002\u548c2:93\u7b97\u6cd5\u76f8\u6bd4\uff0c6:23\u7b97\u6cd5\u7684intron\u6ca1\u6709\u7b2c3\u548c\u7b2c4\u90e8\u5206\uff08\u5bcc\u542bCT\u533a\u57df\u3001\u8fde\u63a5\u533a\uff09\u3002\u540c\u65f6\uff0c6:23\u7b97\u6cd5\u66f4\u9002\u5408\u4e8eDNA\u5e8f\u5217\u4e2d\u6ca1\u6709\u5c4f\u853d\u91cd\u590d\u6216introns\u5e8f\u5217\u6bd4\u8f83\u602a\u5f02\u7684\u60c5\u51b5\u3002\u4f7f\u7528\u8be5\u7b97\u6cd5\u7684\u65f6\u5019\uff0c-intron\u53c2\u6570\u7684\u503c\u5f97\u662ftied\uff08\u4e5f\u662f\u8be5\u53c2\u6570\u9ed8\u8ba4\u7684\u503c\uff09\uff0c\u5426\u5219\u4f1a\u5f97\u5230\u9519\u8bef\u7684\u5f88\u957f\u7684intron\u7ed3\u679c\u3002\r\n3. \u82e5\u662f\u7b97\u6cd5\u540e\u9762\u5e26\u4e2a L \u5b57\u6837\uff0c\u5219\u8868\u793a\u9002\u7528\u4e8e\u8fdb\u884c\u8f93\u5165\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u662f HMM \u6a21\u578b\u3002\u6b64\u5916\uff0c \u8fd8\u6709\u5176\u5b83\u7684\u4e00\u4e9b\u7b97\u6cd5\uff0c\u53ef\u4ee5\u53c2\u8003wise2.pdf\u6587\u4ef6\u3002\r\n4. genewise\u5bf9\u57fa\u56e0\u8fdb\u884c\u9884\u6d4b\u540e\uff0c\u6709\u4e00\u4e2a\u5f97\u5206\u3002\u8be5\u5f97\u5206 = log2(\u9884\u6d4b\u6a21\u578b\u7684\u53ef\u80fd\u6027\/\u968f\u673a\u7ed3\u679c\u7684\u53ef\u80fd\u6027) \u3002\u56e0\u6b64\uff0c0\u8868\u793a\u8be5\u7ed3\u679c\u662f\u4e2a\u968f\u673a\u7684\u7ed3\u679c\uff0c\u4e0d\u53ef\u9760\u7684\u3002\u6839\u636e\u8f6f\u4ef6\u4f5c\u8005\u7684\u7ecf\u9a8c\uff0c\u5f97\u5206\u9ad8\u4e8e35\u7684\u7ed3\u679c\u662f\u975e\u5e38\u53ef\u9760\u7684\uff1b\u5f97\u520625~35\u7684\u7ed3\u679c\u662f\u53ef\u4fe1\u7684\uff1b\u5f97\u520618~25\u7684\u7ed3\u679c\u53ef\u80fd\u4ec5\u9002\u7528\u4e8e\u67d0\u4e9b\u86cb\u767d\u8d28\u5bb6\u65cf\uff1b\u5f97\u5206\u4f4e\u4e8e15\u7684\u662f\u4e0d\u53ef\u4fe1\u7684\u3002\r\n<\/pre>\n
4. GeneWise\u7684\u9ad8\u7ea7\u4f7f\u7528<\/h1>\n
\u7528\u4e34\u8fd1\u7269\u79cd\u7684protein\u5e8f\u5217\u5bf9\u57fa\u56e0\u7ec4\u8fdb\u884chomolog gene\u9884\u6d4b\u7684\u65f6\u5019\uff0c\u9700\u8981\u901a\u8fc7blast\u5c06proteins\u5e8f\u5217\u548c\u57fa\u56e0\u7ec4\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\uff0c\u518d\u63d0\u53d6\u57fa\u56e0\u7ec4\u7684\u76ee\u6807\u57fa\u56e0\u533a\u57df\u548c\u6700\u4f73\u7ed3\u679cprotein\u8fdb\u884cgenewise\u5206\u6790\u3002\u56e0\u6b64\uff0c\u9700\u8981\u81ea\u5df1\u5199\u4e00\u4e9b\u7a0b\u5e8f\u8fdb\u884c\u5e76\u884c\u5316\u7684genewise\u8ba1\u7b97\uff0c\u4ece\u800c\u8fbe\u5230\u5bf9\u5168\u57fa\u56e0\u7ec4\u5927\u6570\u636e\u7684\u5206\u6790\u3002Genewise\u8f6f\u4ef6\u63d0\u4f9b\u4e86\u4e00\u652f\u7a0b\u5e8f\/opt\/biosoft\/wise2.4.1\/src\/perl\/scripts\/blastwise.pl\u7a0b\u5e8f\u80fd\u8fdb\u884c\u8be5\u9879\u5904\u7406\uff08\u6211\u6ca1\u6709\u7528\u8fc7\u8be5\u7a0b\u5e8f\uff0c\u6211\u81ea\u5df1\u5199\u4e86\u60f3\u8981\u7684\u7a0b\u5e8f\uff09\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
1. GeneWise \u7b80\u4ecb Genewise\u4e3b\u8981\u7528\u4e8e\u5c06\u86cb\u767d\u8d28\u5e8f\u5217\u548cDNA\u5e8f\u5217\u8fdb … \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":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2162"}],"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=2162"}],"version-history":[{"count":9,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2162\/revisions"}],"predecessor-version":[{"id":2419,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2162\/revisions\/2419"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2162"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2162"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2162"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}