{"id":2300,"date":"2015-08-25T16:44:11","date_gmt":"2015-08-25T08:44:11","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2300"},"modified":"2015-08-25T16:44:23","modified_gmt":"2015-08-25T08:44:23","slug":"web-apollo-%e4%bd%bf%e7%94%a8%e5%bf%83%e5%be%97","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2300","title":{"rendered":"Web Apollo \u4f7f\u7528\u5fc3\u5f97"},"content":{"rendered":"<p>1. Maker \u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u7efc\u5408\u4e86 Augustus, GeneMarkES \u548c SNAP \u7684 ab initio \u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u548c EST \u4e0e Protein \u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u6240\u4ee5 Maker \u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u6bd4\u8f83\u51c6\u786e\u3002 Augustus \u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u63d0\u4f9b\u4e86 UTR \u9884\u6d4b\u7ed3\u679c\uff0c\u540c\u65f6\u7531\u4e8e\u8f93\u5165\u4e86 intron \u4fe1\u606f\uff0c\u9884\u6d4b\u7684\u7ed3\u679c\u5bf9 intron \u7684\u9884\u6d4b\u5f88\u51c6\u3002GeneMarkES \u7684\u9884\u6d4b\u7ed3\u679c\u5bf9\u771f\u83cc\u662f\u5f88\u51c6\u7684\uff0c\u6bd4 SNAP \u8981\u597d\u3002\u6240\u4ee5\uff0c\u8fdb\u884c\u624b\u5de5\u4fee\u6b63\u7684\u65f6\u5019\uff0c\u4e3a\u4e86\u83b7\u5f97\u6700\u51c6\u786e\u7684\u57fa\u56e0\u7ed3\u6784\uff0c\u82e5\u57fa\u56e0\u6709\u8868\u8fbe\uff0c\u7279\u522b\u6709intron\u8bc1\u636e\u65f6\u5019\uff0c\u4e00\u822c\u4f7f\u7528 Augustus \u7684\u9884\u6d4b\u7ed3\u679c\uff1b\u82e5\u65e0\u8868\u8fbe\u7684\u57fa\u56e0\uff0c\u5f88\u591a\u65f6\u5019\u9009\u62e9 Maker \u6216 GeneMarkES \u7684\u9884\u6d4b\u7ed3\u679c\u3002<br \/>\n2. intron \u7684\u957f\u5ea6\u4e00\u822c\u5728 1000bp \u4ee5\u5185\uff0c 30bp \u4ee5\u4e0a\u3002 \u5982\u679c intron \u957f\u5ea6\u7279\u522b\u957f\uff0c\u5219\u8981\u770b\u6709\u5c11 RNA-Seq \u6570\u636e\u7684\u6bd4\u5bf9\u7ed3\u679c\uff0c\u6709\u591a\u5c11 reads \u80fd\u8de8\u8fc7\u8be5 intron \u3002 \u6ca1\u6709\u8be5\u7c7b\u8bc1\u636e\uff0c\u5219\u8ba4\u4e3a\u8be5 intron \u662f\u9519\u8bef\u7684\u3002<br \/>\n3. \u5c06 RNA-Seq \u6570\u636e\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\uff0c\u8f6c\u6362\u5f97\u5230 BigWig track \u7684\u663e\u793a\u4e2d\uff0c\u8868\u8fbe\u91cf\u96c6\u4e2d\u4e14\u9ad8\u7684\u533a\u57df\u4e00\u822c\u4f4d\u4e8e CDS \u533a\u57df\u3002\u82e5\u9884\u6d4b\u7684\u57fa\u56e0\u5728\u8fd9\u4e9b\u533a\u57df\u662f UTR\uff0c\u5219\u9700\u8981\u6ce8\u610f\u3002<br \/>\n4. \u5728\u8868\u8fbe\u91cf\u6bd4\u8f83\u4f4e\u7684\u533a\u57df\uff0c\u591a\u4e2a\u8f6f\u4ef6\u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u6bd4\u8f83\u6df7\u4e71\u3002\u5728\u8fd9\u4e9b\u533a\u57df\u9009\u62e9\u57fa\u56e0\u7684\u6392\u5e8f\u539f\u5219\u662f\uff1a a) intron \u957f\u5ea6\u592a\u5927\u592a\u5c0f\u7684\u5ffd\u7565\uff1b b) \u6309\u8f6f\u4ef6\u9009\u62e9\u7684\u987a\u5e8f\u662f Augustus > Maker > GeneMarkES > SNAP\uff1b c) \u82e5\u6709\u591a\u4e2a\u8f6f\u4ef6\u7ed9\u7684\u7ed3\u679c\u4e00\u81f4\uff0c\u5219\u9009\u62e9\u4e00\u81f4\u7684\u7ed3\u679c\u3002<br \/>\n5. SNAP\u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u4e2d\u5141\u8bb8\u6709\u5f88\u77ed\u7684 intron\uff0c\u4e2a\u4eba\u89c9\u5f97\u662f\u4e0d\u5bf9\u7684\uff1b SNAP \u9884\u6d4b\u7684\u57fa\u56e0\u957f\u5ea6\u6bd4\u5176\u5b83\u8f6f\u4ef6\u77ed\uff0c\u5bb9\u6613\u6253\u65ad\u57fa\u56e0\u3002<br \/>\n6. Web Apollo \u5728\u975e GTAG intron\u6a21\u5f0f\u5904\u6709\u611f\u53f9\u53f7\u7801\u663e\u793a\u3002 Maker\uff0cSNAP \u548c GeneMarkES \u7b49\u57fa\u56e0\u9884\u6d4b\u8f6f\u4ef6\u4e00\u822c\u4ec5\u8ba4\u53ef GTAG \u7684\u526a\u63a5\u6a21\u5f0f\u3002\u800c\u5b9e\u9645\u4e0a\u5b58\u5728\u5f88\u591a GCAG \u548c ATAC \u6a21\u5f0f\u7684\u526a\u63a5\u6a21\u5f0f\u3002<br \/>\n7. \u4e00\u822c\u60c5\u51b5\u4e0b introns \u5728\u57fa\u56e0\u4e2d\u7684\u4f4d\u7f6e\u5206\u5e03\u6bd4\u8f83\u5747\u5300\uff0c\u957f\u5ea6\u4e5f\u6bd4\u8f83\u5747\u5300\u3002\u5f53 intron \u5728\u57fa\u56e0\u4e2d\u6570\u76ee\u8f83\u591a\u540c\u65f6\u78b1\u57fa\u6bd4\u4f8b\u8f83\u5927\u65f6\u5019\uff0c \u57fa\u56e0\u7ed3\u6784\u50cf\u4e00\u6761\u9c7c\u9aa8\u67b6\u4e00\u6837\u3002\u82e5 introns \u7684\u957f\u5ea6\u4e0d\u5747\u5300\uff0c\u5206\u5e03\u4e0d\u5747\u5300\uff0c\u5219\u57fa\u56e0\u7ed3\u6784\u6781\u53ef\u80fd\u9519\u8bef\u3002<br \/>\n8. Augustus \u9884\u6d4b\u7684\u7ed3\u679c\u548c GeneMarkES \u6bd4\u8f83\u63a5\u8fd1\uff1b Maker \u7efc\u5408\u591a\u4e2a\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u7684\u65f6\u5019\uff0c\u65f6\u5e38\u9009\u62e9 SNAP \u7684\u9884\u6d4b\u7ed3\u679c\u3002<br \/>\n9. \u82e5\u5728\u5c3e\u90e8\u7684\u5c5e\u4e8e UTR \u7684 exon \u975e\u5e38\u77ed\uff0c\u5219\u53bb\u6389\u8be5 exon\uff0c \u751a\u81f3\u53bb\u6389\u8be5\u7aef\u7684 UTR \u533a\u57df\u3002<br \/>\n10. \u6709\u65f6\u5019\u9009\u62e9 PASA \u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\uff0c\u9700\u8981\u9009\u62e9 Set longest ORF\u3002 \u800c\u6709\u65f6\u5019\u9009\u62e9 Augustus \u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\uff0c\u6dfb\u52a0 UTR \u533a\u57df\u540e\uff0c \u7531\u4e8e Web Apollo \u81ea\u52a8\u8bc6\u522b\u6700\u957f\u7684 ORF\uff0c\u4ece\u800c\u4f7f CDS \u533a\u53d1\u751f\u4e86\u6539\u53d8\uff0c\u9700\u8981\u653e\u5927\u5230\u78b1\u57fa\u6c34\u5e73\uff0c\u91cd\u65b0\u8bbe\u5b9a\u8d77\u59cb\u548c\u7ec8\u6b62\u5bc6\u7801\u5b50\uff08\u800c\u4e0d\u662f\u9009\u62e9\u6700\u957f\u7684 ORF\uff09\u3002<br \/>\n11. \u5f53\u57fa\u56e0\u7ec4\u4e00\u4e2a\u533a\u57df\uff0c\u6709\u7684\u8f6f\u4ef6\u9884\u6d4b\u662f 1 \u4e2a\u57fa\u56e0\uff0c\u6709\u7684\u9884\u6d4b\u4e3a\u591a\u4e2a\u3002 \u82e5\u9884\u6d4b\u7684 1 \u4e2a\u57fa\u56e0\u4e2d\u6709\u4e2a\u8fc7\u957f\u7684 intron\uff0c\u5e76\u4e14\u4ec5\u4ec5\u53ea\u6709\u5c11\u6570\u9884\u6d4b\u7ed3\u679c\u662f 1 \u4e2a\u57fa\u56e0\uff0c\u5219\u9700\u8981\u6253\u65ad\uff0c\u8ba4\u4e3a\u8be5\u533a\u57df\u662f\u591a\u4e2a\u57fa\u56e0\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. Maker \u7684\u57fa\u56e0\u9884\u6d4b\u7ed3\u679c\u7efc\u5408\u4e86 Augustus, GeneMarkES &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2300\">\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":[3],"tags":[72],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2300"}],"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=2300"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2300\/revisions"}],"predecessor-version":[{"id":2301,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2300\/revisions\/2301"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2300"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2300"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2300"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}