{"id":1284,"date":"2013-05-10T08:15:58","date_gmt":"2013-05-10T00:15:58","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1284"},"modified":"2013-05-22T16:27:08","modified_gmt":"2013-05-22T08:27:08","slug":"snap%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=1284","title":{"rendered":"SNAP\u7684\u5b89\u88c5\u548c\u4f7f\u7528"},"content":{"rendered":"<h1>1. <a href=\"http:\/\/korflab.ucdavis.edu\/software.html\" target=\"_blank\">SNAP<\/a>\u7b80\u4ecb<\/h1>\n<p>SNAP\u662f<a href=\"http:\/\/korflab.ucdavis.edu\/bio_ian.html\" target=\"_blank\">Ian Korf<\/a>\u72ec\u81ea\u5f00\u53d1\u7684\u8f6f\u4ef6\uff0c\u7b80\u5355\u6613\u7528\u3002<\/p>\n<h1>2. SNAP\u7684\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/korflab.ucdavis.edu\/Software\/snap-2013-02-16.tar.gz\r\n$ tar zxf snap-2013-02-16.tar.gz\r\n$ cd snap\r\n$ make\r\n<\/pre>\n<h1>3. SNAP\u7684Parameter Estimation<\/h1>\n<p><strong>3.1 \u9700\u8981 genes that are not too related to each other\u3002\u548cAUGUSTUS\u4e00\u81f4\uff0c\u57fa\u56e0\u4e24\u4e24\u4e4b\u95f4\u7684identity\u4e0d\u8981\u8d85\u8fc780%\u3002Gene structures must be in ZFF format.<\/strong><\/p>\n<p>ZFF\u683c\u5f0f\u662fIan Korf\u81ea\u884c\u4f7f\u7528\u7684\u4e00\u4e2a\u683c\u5f0f\uff0c\u6709\u957f\u77ed\u4e24\u79cd\u683c\u5f0f\u3002In the short format, there are 4 fields: Label, Begin, End, Group.if Begin > End, the feature is on the minus strand.<\/p>\n<pre>\r\n>sequence-1\r\nEinit    201    325   Y73E7A.6\r\nEterm   2175   2319   Y73E7A.6\r\n>sequence-2\r\nEinit    201    462   Y73E7A.7\r\nExon    1803   2031   Y73E7A.7\r\nExon    2929   3031   Y73E7A.7\r\nExon    3467   3624   Y73E7A.7\r\nExon    4185   4406   Y73E7A.7\r\nEterm   5103   5280   Y73E7A.7\r\n<\/pre>\n<p>\u4e0d\u7ba1\u662f\u5728\u6b63\u94fe\uff0c\u8fd8\u662f\u8d1f\u94fe\uff0c\u4ece\u4e0a\u5230\u4e0b\uff0c\u8d77\u59cb\u4f4d\u7f6e\u662f\u9010\u6e10\u53d8\u5927\u7684\uff1b\u5982\u679c\u662f\u5728\u6b63\u94fe\u4e0a\uff0cBegin > End, Einit\u5728Eterm\u524d\u9762\uff1b\u5982\u679c\u662f\u5728\u8d1f\u94fe\u4e0a\uff0c\u5219 Begin < End, Eterm\u5728Einit\u524d\u9762\u3002\n\n<strong>3.2 \u505aParameter Estimation\u9700\u8981\u4e00\u5b9a\u6570\u76ee\u7684genes\uff0c\u8fd9\u4e9bgenes\u7684ZFF\u6587\u4ef6\u548c\u76f8\u5e94\u7684genome\u5e8f\u5217\u6587\u4ef6\u3002<\/strong><\/p>\n<p>\u6ce8\u610fgeneome\u5e8f\u5217\u6587\u4ef6\u53ea\u662f\u5305\u542b\u6709\u8fd9\u4e9b\u57fa\u56e0\u7684\u5e8f\u5217\uff0c\u5982\u679c\u542b\u6709\u5176\u5b83\u7684\u5e8f\u5217\u7684\u8bdd\uff0c\u7a0b\u5e8f\u8fd0\u884c\u4f1a\u51fa\u95ee\u9898\uff08core dump\u7b49\uff09\u3002<\/p>\n<p>\u4f7f\u7528gff3_to_zff.pl\u6765\u5c06gff3\u6587\u4ef6\u8f6c\u6362\u6210zff\u6587\u4ef6; \u518d\u4f7f\u7528order.pl\u6765\u8c03\u6574Einit, Exon, Eterm\u7684\u987a\u5e8f\u3002<\/p>\n<pre>\r\n$ <a href=\"http:\/\/gremlin2.soic.indiana.edu\/blog\/?p=758\" target=\"_blank\">.\/gff3_to_zff.pl<\/a> genes.gff3 > genes.zff\r\n$ .\/order.pl genes.zff > species.ann\r\n<\/pre>\n<p>\u63d0\u53d6\u51fa\u76f8\u5e94\u7684genome\u7684\u5e8f\u5217,\u5e76\u5bf9\u5176\u8fdb\u884c\u6392\u5e8f\uff1a<\/p>\n<pre>\r\n$ grep '^>' species.ann | tr -d '>' > species.seqs2keep\r\n$ .\/fasta_sort.pl species.seqs2keep < geome.fasta > species.dna\r\n<\/pre>\n<p><strong>3.3 \u68c0\u6d4bgenes\u4e2d\u7684\u9519\u8bef\u548c\u8b66\u793a\uff0c\u7136\u540e\u5bf9genes\u8fdb\u884c\u4fee\u6b63\u6216\u4e22\u5f03<\/strong><\/p>\n<pre>\r\n$ $SnapHome\/fathom species.ann species.dna -gene-stats &> gene-stats.log\r\n$ $SnapHome\/fathom species.ann species.dna -validate &> validate.log\r\n\r\n$ grep OK validate.log > species.zff2keep\r\n$ perl -p -i -e 's\/.*:\\s+(\\S+)\\s+OK\/$1\/' species.zff2keep\r\n$ .\/filterGenes.pl species.zff2keep species.ann > tmp\r\n$ mv tmp species.ann\r\n<\/pre>\n<p><strong>3.4 \u5c06\u5e8f\u5217\u6253\u65ad\u6210\u4e00\u4e2a\u5e8f\u5217\u4e00\u4e2agene\u7684\u7247\u6bb5\uff0c\u5728CDS\u4e24\u7aef\u5404\u52a01000bp\u957f\u5ea6\u5e8f\u5217\uff0c\u5e76\u5c06\u6240\u6709\u7684genes\u8f6c\u6362\u5230\u6b63\u4e49\u94fe\u4e0a\u3002<\/strong><\/p>\n<pre>\r\n$ $SnapHome\/fathom species.ann species.dna -categorize 1000\r\n$ $SnapHome\/fathom species.ann species.dna -export 1000\r\n<\/pre>\n<p><strong>3.5 run the parameter estimation program<\/strong><\/p>\n<pre>\r\n$ mkdir params; cd params\r\n$ $SnapHome\/forge ..\/export.ann ..\/export.dna \r\n$ cd ..\r\n<\/pre>\n<p><strong>3.6 Last is to build an HMM<\/strong><\/p>\n<pre>\r\n$ $SnapHome\/hmm-assembler.pl species params > species.hmm\r\n<\/pre>\n<p>SNAP\u7684Parameter Estimation\u80fd\u5f88\u5feb\u5730\u5b8c\u6210\u3002\u4e0d\u50cfAUGUSTUS\u90a3\u6837\u8017\u65f6\u3002<\/p>\n<h1>4. \u8fd0\u884csnap\u8fdb\u884c\u57fa\u56e0\u9884\u6d4b<\/h1>\n<pre>\r\n$ $SnapHome\/snap species.hmm species.geonme > species.zff\r\n$ $SnapHome\/zff2gff3.pl species.zff > species.gff3\r\n<\/pre>\n<h1>5. \u5c06\u9884\u6d4b\u7684zff\u7ed3\u679c\u8f6c\u6362\u6210gff3\u7ed3\u679c<\/p>\n<h1>\n\u57284\u4e2d\u8f6c\u6362\u6210\u7684gff3\u6587\u4ef6\u7684\u6700\u540e\u4e00\u5217attributes\u4e2d\uff0c\u53ea\u6709Name\u6807\u7b7e\u3002\u800c\u4f7f\u7528EVM\u8f6f\u4ef6\u5c06\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u878d\u5408\u7684\u65f6\u5019\uff0c\u9700\u8981\u7684gff3\u6587\u4ef6\u4e2d\u8be5\u5217\u7684\u6807\u7b7e\u6709ID\u548cParent\uff0c\u56e0\u6b64\u9700\u8981\u5176\u5b83\u7684\u65b9\u6cd5\u6765\u5c06zff\u6587\u4ef6\u8f6c\u6362\u6210gff3\u6587\u4ef6\u3002\u53ef\u4ee5\u4f7f\u7528EVM\u5305\u542b\u7684\u4e00\u4e2aperl\u7a0b\u5e8f\u6765\u89e3\u51b3\u3002<\/p>\n<p>\u4f7f\u7528\u8be5\u7a0b\u5e8f\u9700\u8981\u5148\u5c06EVM\u81ea\u5e26\u7684\u4e00\u4e9bperl\u6a21\u5757export\u5230\u5176\u8def\u5f84\uff1b\u540c\u65f6\u9700\u8981\u5b89\u88c5<a href=\"http:\/\/sourceforge.net\/projects\/cdbfasta\/?source=dlp\" target=\"_blank\">cdbfasta<\/a><\/p>\n<pre>\r\n$EVMHome\/OtherGeneFinderTrainingGuid\/SNAP\/SNAP_output_to_gff3.pl species.zff species.geome > species.gff3\r\n<\/pre>\n<p>SNAP\u57fa\u56e0ab initio\u7684\u57fa\u56e0\u9884\u6d4b\u901f\u5ea6\u5f88\u5feb\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. SNAP\u7b80\u4ecb SNAP\u662fIan Korf\u72ec\u81ea\u5f00\u53d1\u7684\u8f6f\u4ef6\uff0c\u7b80\u5355\u6613\u7528\u3002 2.  &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1284\">\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":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1284"}],"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=1284"}],"version-history":[{"count":7,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1284\/revisions"}],"predecessor-version":[{"id":1322,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1284\/revisions\/1322"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1284"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1284"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1284"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}