{"id":2323,"date":"2015-08-25T16:55:40","date_gmt":"2015-08-25T08:55:40","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2323"},"modified":"2015-08-25T16:55:40","modified_gmt":"2015-08-25T08:55:40","slug":"maker%e7%9a%84%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2323","title":{"rendered":"MAKER\u7684\u4f7f\u7528"},"content":{"rendered":"

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

MAKER <\/a>\u662f\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ed3\u6784\u6ce8\u91ca\u7684\u4e00\u6574\u5957\u6d41\u7a0b\u3002\u5b83\u7efc\u5408\u4e86ab initio\u65b9\u6cd5\u548c evidence \u7684\u65b9\u6cd5\u8fdb\u884c\u57fa\u56e0\u7ec4\u6ce8\u91ca\u3002\u4f7f\u7528\u8d77\u6765\u975e\u5e38\u65b9\u4fbf\u5feb\u6377\uff0c\u4e00\u4e2a\u547d\u4ee4\u80fd\u641e\u5b9a\u5168\u5957\u57fa\u56e0\u7ec4\u7ed3\u6784\u6ce8\u91ca\u3002<\/p>\n

2. MAKER\u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h1>\n

\u5728http:\/\/yandell.topaz.genetics.utah.edu\/cgi-bin\/maker_license.cgi<\/a>\u9875\u9762\u63d0\u4ea4\u4fe1\u606f\u5e76\u4e0b\u8f7d\u6700\u65b0\u7248\u672cMAKER\u3002<\/p>\n

\u6b64\u5916\uff0c\u5b89\u88c5 maker \u9700\u8981\u5148\u5b89\u88c5\u4e00\u4e9b\u8f6f\u4ef6<\/a>\uff1a<\/p>\n

\r\n\u5fc5\u987b\u5b89\u88c5\uff1a\r\nPerl 5.8.0 or higher\r\nBioPerl 1.6 or higher\r\nWU-BLAST 2.0 or higher or NCBI-BLAST 2.2.X or higher \r\nRepeatMasker 3.1.6 or higher\r\n    RepeatMasker requires a repeat library, available from Repbase. \r\nExonerate 1.4 or higher\r\n\r\n\u53ef\u9009\u5b89\u88c5\uff1a\r\nSNAP version 2009-02-03 or higher (for eukaryotic genomes).\r\nAugustus 2.0 or higher (for eukaryotic genomes) \r\nGeneMark-ES (for eukaryotic genomes)\r\nFGENESH 2.6 or higher - requires licence (for eukaryotic genomes)\r\nGeneMarkS (for prokaryotic genomes) \r\nsnoscan\r\nMPICH2 \uff08install MPICH2 with the --enable-sharedlibs flag\uff09\r\n<\/pre>\n
\r\n\u5b89\u88c5perl\u6a21\u5757\r\n$ cpan -i BioPerl Bit::Vector DBD::SQLite DBI Error Error::Simple File::NFSLock File::Which forks forks::shared Inline Inline::C IO::All IO::Prompt PerlIO::gzip Perl::Unsafe::Signals Proc::ProcessTable Proc::Signal threads URI::Escape\r\n\r\n\u5b89\u88c5mpich2\r\n$ sudo yum install mpich2*\r\n\u4f7f\u7528 MPI \u8fd0\u884c Maker \u9700\u8981\u5148\u8fd0\u884c\u670d\u52a1 mpd\u3002\r\n\u6b63\u5e38\u8fd0\u884c mpd \u547d\u4ee4\uff0c\u9700\u8981\u6b63\u786e\u7684\u4e3b\u673a\u540d\u3002\u5426\u5219\u53ef\u80fd\u4f1a\u9047\u5230\u62a5\u9519\u3002\u9700\u8981\u4fee\u6539 \/etc\/hosts \u6587\u4ef6\uff0c\u5c06\u4e3b\u673a\u540d\u7684 IP \u5bf9\u5e94\u6b63\u786e\u3002\r\n\r\n\u5b89\u88c5maker\r\n$ wget http:\/\/yandell.topaz.genetics.utah.edu\/maker_downloads\/2D3B\/22C6\/BE99\/41DBB7F9B1D181B2CDCE1E49DFE6\/maker-2.31.8.tgz\r\n$ tar zxf maker-2.31.8.tgz \r\n$ cd maker\/src\/\r\n$ perl Build.PL \r\n$ .\/Build install\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/maker\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc \r\n<\/pre>\n
3. MAKER \u7684\u4f7f\u7528<\/h1>\n
3.1 \u51c6\u5907 MAKER \u7684\u8f93\u5165\u6587\u4ef6<\/h2>\n
MAKER \u9700\u8981\u7684\u8f93\u5165\u6587\u4ef6\u5982\u4e0b\uff1a<\/p>\n
\r\n1. genome.fasta\r\n    \u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6\u3002\r\n2. inchworm.fasta\r\n    \u8f6c\u5f55\u7ec4\u7ec4\u88c5\u7ed3\u679c\u6587\u4ef6\u3002\u6b64\u6587\u4ef6\u5185\u5bb9\u4ee3\u8868\u8f6c\u5f55\u5b50\u5e8f\u5217\u6216 EST \u5e8f\u5217\u3002\u4e3a\u4e86\u589e\u52a0\u5176\u51c6\u786e\u6027\uff0c\u6211\u4e2a\u4eba\u9009\u7528\u4e86 trinity \u4e2d inchworm \u7684\u7ed3\u679c\u6587\u4ef6\uff0c\u800c\u4e0d\u662f\u8f6c\u5f55\u7ec4\u6700\u7ec8\u7684\u7ec4\u88c5\u7ed3\u679c\u6587\u4ef6\u3002\r\n3. proteins.fasta\r\n    \u4e34\u8fd1\u7269\u79cd\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u3002\u53ef\u4ee5\u4ece NCBI \u7684 Taxonomy \u6570\u636e\u5e93\u4e2d\u4e0b\u8f7d\u3002\r\n4. consensi.fa.classified\r\n    \u9002\u5408\u672c\u7269\u79cd\u7684\u91cd\u590d\u5e8f\u5217\u6570\u636e\u5e93\u3002\u8be5\u6587\u4ef6\u662f\u4e00\u4e2afasta\u6587\u4ef6\uff0c\u5176\u5e8f\u5217\u4ee3\u8868\u7740\u672c\u7269\u79cd\u7684\u9ad8\u91cd\u590d\u5e8f\u5217\u3002\u8be5\u6587\u4ef6\u4f7f\u7528 RepeatModeler \u5236\u4f5c\u3002\r\n5. Augustus hmm files [species]\r\n    \u9002\u5408\u672c\u7269\u79cd\u7684 Augustus \u7684 HMM \u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u4ee5\u6587\u4ef6\u5939\u5f62\u5f0f\u5b58\u653e\u5728 \/opt\/biosoft\/augustus-3.0.3\/config\/species\/ \u76ee\u5f55\u4e0b\u3002\u5c06 genome.fasta \u548c inchworm.fasta \u8f93\u5165 PASA\uff0c\u5f97\u5230\u7528\u4e8e trainning \u7684\u57fa\u56e0\uff0c\u7136\u540e\u4f7f\u7528 Augustus \u8fdb\u884c training\uff0c\u5f97\u5230 HMM \u6587\u4ef6\u3002\r\n6. Snap hmm file [species.hmm]\r\n    \u9002\u5408\u672c\u7269\u79cd\u7684 SNAP \u7684 HMM \u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u662f\u4e00\u4e2a\u5355\u72ec\u7684\u6587\u4ef6\u3002\u5c06 genome.fasta \u548c inchworm.fasta \u8f93\u5165 PASA\uff0c\u5f97\u5230\u7528\u4e8e trainning \u7684\u57fa\u56e0\uff0c\u7136\u540e\u4f7f\u7528 SNAP \u8fdb\u884c training\uff0c\u5f97\u5230 HMM \u6587\u4ef6\u3002\r\n7. Genemark_es hmm file [es.mod]\r\n    \u9002\u5408\u672c\u7269\u79cd\u7684 Genemark_es \u7684 HMM \u6587\u4ef6\u3002\u5c06 genome.fasta \u8f93\u5165 genemark_es \u8f6f\u4ef6\u8fdb\u884c\u81ea\u6211\u8bad\u7ec3\u5f97\u5230\u7684 HMM \u6587\u4ef6\u3002\r\n8. rRNA.fa\r\n    rRNA \u7684\u5e8f\u5217\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u4f7f\u7528 RNAmmer \u5bf9\u57fa\u56e0\u7ec4\u8fdb\u884c\u5206\u6790\u5f97\u5230\u3002\r\n<\/pre>\n
\u5f97\u5230\u4e0a\u8ff0\u8f93\u5165\u6587\u4ef6\u540e\uff0c\u4f7f\u7528 MAKER \u547d\u4ee4\u5f97\u5230\u521d\u59cb\u5316\u7684 3 \u4e2a\u914d\u7f6e\u6587\u4ef6\u3002<\/p>\n
\r\n$ maker -CTL\r\n\r\n\u5f97\u52303\u4e2a\u914d\u7f6e\u6587\u4ef6\uff1a maker_exe.ctl, maker_bopts.ctl \u548c maker_opts.ctl\u3002\r\nmaker_exe.ctl\uff1a \u914d\u7f6e Maker \u9700\u8981\u8c03\u7528\u7684\u7a0b\u5e8f\u7684\u8def\u5f84\r\nmaker_bopts.ctl\uff1a \u914d\u7f6e blast \u7684\u5404\u79cd\u9608\u503c\r\nmaker_opts.ctl\uff1a MAKER \u7684\u4e3b\u8981\u914d\u7f6e\u6587\u4ef6\uff0c\u914d\u7f6e\u8f93\u5165\u6587\u4ef6\u7684\u8def\u5f84\uff0c\u4ee5\u53ca MAKER \u7684\u4f7f\u7528\u6d41\u7a0b\u3002\r\n<\/pre>\n
3.2 \u4f7f\u7528 MAKER \u8fdb\u884c\u57fa\u56e0\u7ec4\u6ce8\u91ca<\/h2>\n
\u5148\u4fee\u6539 maker_opts.ctl \u914d\u7f6e\u6587\u4ef6\uff0c\u9700\u8981\u4fee\u6539\u7684\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n
\r\ngenome=genome.fasta            # \u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6\r\nest=inchworm.fasta             # EST \u5e8f\u5217\u6587\u4ef6\r\nprotein=proteins.fasta         # \u4e34\u8fd1\u7269\u79cd\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u6587\u4ef6\r\nmodel_org=fungi                # \u9009\u62e9repebase\u6570\u636e\u5e93\u7684\u7269\u79cd\uff0c\u5bf9\u771f\u83cc\u5219\u7528fungi\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 all\r\nrmlib=consensi.fa.classified   # \u9002\u5408\u672c\u7269\u79cd\u7684\u91cd\u590d\u5e8f\u5217\u6570\u636e\u5e93\r\nsnaphmm=species.hmm            # snap traing \u7684 HMM \u6587\u4ef6\r\ngmhmm=es.mod                   # genemark_es \u7684 HMM \u6587\u4ef6\r\naugustus_species=species       # augustus \u7684 HMM \u6587\u4ef6\r\nest2genome=1                   # \u4f7f\u7528 EST \u5e8f\u5217\u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\r\nprotein2genome=1               # \u4f7f\u7528\u86cb\u767d\u8d28\u5e8f\u5217\u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\r\ntrna=1                         # \u4f7f\u7528 tRNAscan \u8fdb\u884c tRNA \u9884\u6d4b\r\nsnoscan_rrna=rRNA.fa           # \u4f7f\u7528 Snoscan \u5229\u7528 rRNA \u5e8f\u5217\u8fdb\u884c C\/D box \u7c7b\u578b\u7684 snoRNAs \u9884\u6d4b\uff0c\u4e0d\u8fc7\u6211\u52a0\u5165\u4e86\u8fd9\u4e2a\u4fe1\u606f\u540e\uff0cmaker\u8fd0\u884c\u4e0d\u6210\u529f\uff0c\u4e0d\u77e5\u9053\u4e3a\u4ec0\u4e48\u3002\r\ncorrect_est_fusion=1           # \u8fdb\u884c\u878d\u5408 EST \u7684\u6821\u6b63\r\n<\/pre>\n
\u5e76\u884c\u5316\u8fd0\u884c maker\u3002\u7531\u4e8e\u57fa\u56e0\u7ec4\u5e8f\u5217\u6bd4\u8f83\u5927\uff0cMAKER \u7684\u8ba1\u7b97\u91cf\u5927\uff0c\u4f7f\u7528\u5e76\u884c\u5316\u80fd\u6781\u5927\u8282\u7ea6\u65f6\u95f4\u3002<\/p>\n
\r\n$ mpd &\r\n$ maker                  # \u4e0d\u5e76\u884c\u5316\u8fd0\u884c\r\n$ mpiexec -n 20 maker    # \u4f7f\u752820\u4e2a\u7ebf\u7a0b\u5e76\u884c\u8ba1\u7b97\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. MAKER \u7b80\u4ecb MAKER \u662f\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ed3\u6784\u6ce8\u91ca\u7684\u4e00\u6574\u5957\u6d41\u7a0b\u3002\u5b83\u7efc\u5408\u4e86a … \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":[72],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2323"}],"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=2323"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2323\/revisions"}],"predecessor-version":[{"id":2324,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2323\/revisions\/2324"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2323"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2323"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2323"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}