{"id":2311,"date":"2015-08-25T16:48:53","date_gmt":"2015-08-25T08:48:53","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2311"},"modified":"2015-08-25T16:48:53","modified_gmt":"2015-08-25T08:48:53","slug":"%e5%9f%ba%e5%9b%a0%e9%a2%84%e6%b5%8b%e6%b5%81%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2311","title":{"rendered":"\u57fa\u56e0\u9884\u6d4b\u6d41\u7a0b"},"content":{"rendered":"<h1>1. \u83b7\u53d6\u51c6\u786e\u7684\u8f6c\u5f55\u5b50\u5e8f\u5217<\/h1>\n<p>\u5229\u7528 RNA-seq \u6570\u636e\u8fdb\u884c\u8f6c\u5f55\u7ec4 <em>de novo<\/em> \u7ec4\u88c5\u3002 \u63a8\u8350\u4f7f\u7528 trinity \u8f6f\u4ef6\u8fdb\u884c\u6709\u57fa\u56e0\u6307\u5bfc\u7684 <em>de novo<\/em> \u7ec4\u88c5\uff0c\u53ea\u8fdb\u884c inchworm \u7ec4\u88c5\uff0c\u8fd9\u6837\u80fd\u83b7\u5f97\u6bd4\u8f83\u51c6\u786e\u7684\u8f6c\u5f55\u7ec4\u5e8f\u5217\u3002<\/p>\n<h1>2. \u83b7\u53d6\u5b8c\u6574\u7684\u57fa\u56e0\u6a21\u578b<\/h1>\n<p>\u4f7f\u7528 PASA \u5c06\u4e0a\u4e00\u6b65\u9aa4\u5f97\u5230\u7684\u8f6c\u5f55\u5b50\u5e8f\u5217\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u4e0a\u3002\u6839\u636e\u6bd4\u5bf9\u7ed3\u679c\uff0c\u63d0\u53d6\u5b8c\u6574\u5e76\u4e14\u957f\u5ea6\u8f83\u957f\u7684\u57fa\u56e0\u6a21\u578b\u3002<\/p>\n<h1>3. HMM training<\/h1>\n<p>\u6839\u636e\u4e0a\u4e00\u6b65\u9aa4\u7684\u57fa\u56e0\u6a21\u578b\u8fdb\u884c AUGUSTUS \u548c SNAP \u7684 training\uff0c\u5f97\u5230\u8fd9 2 \u4e2a\u57fa\u56e0\u9884\u6d4b\u8f6f\u4ef6\u7684 HMM \u53c2\u6570\u6587\u4ef6\u3002<\/p>\n<h1>4. \u7531 RNA-seq \u6570\u636e\u5f97\u5230 hints<\/h1>\n<p>\u5bf9\u57fa\u56e0\u7ec4\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u5206\u6790\uff0c\u5bf9 DNA \u8f6c\u5ea7\u5b50\u548c\u9006\u8f6c\u5f55\u8f6c\u5ea7\u5b50\u8fdb\u884c hardmask (\u5373\u5bf9\u8be5\u533a\u57df\u4f7f\u7528 N \u5c4f\u853d)\uff0c\u5bf9 low-complexity \u533a\u57df\u8fdb\u884c softmask(\u5373\u5c06\u8be5\u533a\u57df\u78b1\u57fa\u6362\u6210\u5c0f\u5199)\u3002 \u5c06 RNA-seq \u6570\u636e\u6bd4\u5bf9\u5230\u5c4f\u853d\u4e86\u91cd\u590d\u5e8f\u5217\u7684\u57fa\u56e0\u7ec4\uff0c\u5f97\u5230 hints \u4fe1\u606f\u3002<\/p>\n<h1>5. \u83b7\u53d6\u4f4e\u8868\u8fbe\u533a\u57df\u6765\u81ea\u5176\u5b83\u7269\u79cd\u7684\u4fdd\u5b88\u86cb\u767d<\/h1>\n<p>\u5728\u5c4f\u853d\u91cd\u590d\u5e8f\u5217\u7684\u57fa\u7840\u4e0a\uff0c\u5bf9\u4e0a\u4e00\u6b65\u9aa4\u5f97\u5230 hints \u533a\u57df\u8fdb\u884chardmask\u3002 \u4ece NCBI \u7684 Taxonomy \u6570\u636e\u5e93\u4e0b\u8f7d\u86cb\u767d\u8d28\u5e8f\u5217\uff0c\u5e76\u5c06\u8fd9\u4e9b\u5e8f\u5217\u6bd4\u5bf9\u5230\u5c4f\u853d\u4e86\u91cd\u590d\u5e8f\u5217\u548c\u57fa\u56e0\u8868\u8fbe\u533a\u57df\u7684\u57fa\u56e0\u7ec4\u4e0a\uff0c\u8bbe\u5b9a\u9608\u503c\u7b5b\u9009\u51fa\u4fdd\u5b88\u86cb\u767d\u3002\u8fd9\u4e9b\u86cb\u767d\u6bd4\u5bf9\u5230\u4e86\u8868\u8fbe\u91cf\u4f4e\u7684\u57fa\u56e0\u533a\uff0c\u6709\u5229\u4e8e\u8fd9\u4e9b\u57fa\u56e0\u7684\u9884\u6d4b\u3002<\/p>\n<h1>6. \u4f7f\u7528 MAKER \u8fdb\u884c\u7b2c\u4e00\u904d\u57fa\u56e0\u9884\u6d4b<\/h1>\n<p>\u4f7f\u7528 MAKER \u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\uff0c\u8f93\u5165\u6587\u4ef6\u6709\uff1a <\/p>\n<pre>\r\n\u57fa\u56e0\u7ec4\u5e8f\u5217\uff1a \u57fa\u56e0\u7ec4\u88c5\u7684\u7ed3\u679c\u6587\u4ef6\r\n\u91cd\u590d\u5e8f\u5217\u6587\u5e93\uff1a \u4f7f\u7528 ReapeterModeler \u5f97\u5230\r\nHMM \u6587\u4ef6\uff1a AUGUSTUS, SNPA \u548c GeneMark-ES \u7684 HMM \u6587\u4ef6\r\n\u8f6c\u5f55\u5b50\u5e8f\u5217\uff1a PASA \u7684\u7ed3\u679c\u6587\u4ef6\r\n\u86cb\u767d\u8d28\u5e8f\u5217\uff1a \u7b5b\u9009\u51fa\u6765\u7684\u86cb\u767d\u5e8f\u5217\r\n<\/pre>\n<h1>7. \u4f7f\u7528 MAKER \u8fdb\u884c\u7b2c\u4e8c\u904d\u57fa\u56e0\u9884\u6d4b<\/h1>\n<p>\u6839\u636e\u4e0a\u4e00\u6b65\u7684\u9884\u6d4b\u7ed3\u679c\uff0c\u63d0\u53d6 AED \u503c\u8f83\u4f4e\u7684\u57fa\u56e0\u6a21\u578b\uff0c\u8fdb\u884c\u7b2c\u4e8c\u904d HMM training\uff0c\u7136\u540e\u518d\u6b21\u4f7f\u7528 MAKER \u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\u3002<\/p>\n<h1>8. \u8fdb\u884c\u57fa\u56e0\u6a21\u578b\u7684\u4eba\u5de5\u6821\u6b63<\/h1>\n","protected":false},"excerpt":{"rendered":"<p>1. \u83b7\u53d6\u51c6\u786e\u7684\u8f6c\u5f55\u5b50\u5e8f\u5217 \u5229\u7528 RNA-seq \u6570\u636e\u8fdb\u884c\u8f6c\u5f55\u7ec4 de novo &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2311\">\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\/2311"}],"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=2311"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2311\/revisions"}],"predecessor-version":[{"id":2312,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2311\/revisions\/2312"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2311"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2311"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2311"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}