{"id":2349,"date":"2015-08-25T17:08:43","date_gmt":"2015-08-25T09:08:43","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2349"},"modified":"2015-08-25T17:08:43","modified_gmt":"2015-08-25T09:08:43","slug":"agp%e6%a0%bc%e5%bc%8f%e7%ae%80%e5%8d%95%e8%af%b4%e6%98%8e","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2349","title":{"rendered":"AGP\u683c\u5f0f\u7b80\u5355\u8bf4\u660e"},"content":{"rendered":"<p>AGP\u6587\u4ef6\u4e3aNCBI\u6570\u636e\u4e0a\u4f20\u8981\u6c42\u7684\u6807\u51c6\u683c\u5f0f\uff0c\u7528\u6765\u63cf\u8ff0\u5c0f\u7247\u6bb5\u5e8f\u5217\uff08\u6bd4\u5982contig\uff09\u5982\u4f55\u6784\u6210\u5927\u7247\u6bb5\u5e8f\u5217\uff08\u6bd4\u5982scaffold\u548cchromosome\uff09\u3002\u8be6\u7ec6\u7684\u8bf4\u660e\u6587\u6863\u8bf7\u89c1\uff1a<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/projects\/genome\/assembly\/agp\/AGP_Specification.shtml\" target=\"_blank\">http:\/\/www.ncbi.nlm.nih.gov\/projects\/genome\/assembly\/agp\/AGP_Specification.shtml<\/a><br \/>\nAGP\u6587\u4ef6\u67099\u5217\uff0c\u5206\u522b\u662f\uff1a<\/p>\n<pre>\r\n1. \u5927\u7247\u6bb5\u7684\u5e8f\u5217\u540d(object)\r\n2. \u5927\u7247\u6bb5\u8d77\u59cb(object_begin)\r\n3. \u5927\u7247\u6bb5\u7ed3\u675f(object_end)\r\n4. \u8be5\u6bb5\u5e8f\u5217\u5728\u5927\u7247\u6bb5\u4e0a\u7684\u7f16\u53f7(part_number)\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u4e00\u822c\u4e00\u4e2a\u5927\u7247\u6bb5\u7531\u591a\u4e2a\u5c0f\u7247\u6bb5\u548cgap\u7ec4\u6210\u3002\u6b64\u5904\u5219\u4e3a\u8fd9\u4e9b\u5c0f\u7247\u6bb5\u548cgap\u5728\u5927\u7247\u6bb5\u4e0a\u7684\u7f16\u53f7\u3002\r\n5. \u8be5\u6bb5\u5e8f\u5217\u7684\u7c7b\u578b(component_type)\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u5e38\u7528\u7684\u662fW\u3001N\u548cU\u3002W\u8868\u793aWGS contig\uff1bN\u8868\u793a\u6307\u5b9a\u5927\u5c0f\u7684gap\uff1bU\u8868\u793a\u4e0d\u660e\u786e\u957f\u5ea6\u7684gap\uff0c\u4e00\u822c\u7528100bp\u957f\u5ea6\u3002\r\n6. \u5c0f\u7247\u6bb5\u7684ID\u6216gap\u957f\u5ea6(component_id or gap_length)\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u5982\u679c\u7b2c5\u5217\u4e0d\u4e3aN\u6216U\uff0c\u5219\u6b64\u5217\u4e3a\u5c0f\u7247\u6bb5\u7684ID\u3002\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u5982\u679c\u7b2c5\u5217\u662fN\u6216U\uff0c\u5219\u6b64\u5217\u4e3agap\u7684\u957f\u5ea6\u3002\u5982\u679c\u7b2c5\u5217\u4e3aU\uff0c\u5219\u6b64\u5217\u503c\u5fc5\u987b\u4e3a100\u3002\r\n7. \u5c0f\u7247\u6bb5\u8d77\u59cb\u6216gap\u7c7b\u578b(component_begin or gap_type)\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u5982\u679c\u7b2c5\u5217\u662fN\u6216U\uff0c\u5219\u6b64\u5217\u8868\u793agap\u7684\u7c7b\u578b\u3002\u5e38\u7528\u7684\u503c\u662fscaffold\uff0c\u8868\u793a\u662fscaffold\u51852\u4e2acontigs\u4e4b\u95f4\u7684gap\u3002\u5176\u5b83\u503c\u6709\uff1acontig\uff0c2\u4e2acontig\u5e8f\u5217\u4e4b\u95f4\u7684unspanned gap\uff0c\u8fd9\u6837\u7684gap\u7531\u4e8e\u6ca1\u6709\u8bc1\u636e\u8868\u660e\u6709gap\uff0c\u5e94\u8be5\u8981\u6253\u65ad\u5927\u7247\u6bb5\u5e8f\u5217\uff1bcentromere\uff0c\u8868\u793a\u4e2d\u5fc3\u7c92\u7684gap\uff1bshort_arm\uff0ca gap inserted at the start of an acrocentric chromosome\uff1bheterochromatin\uff0ca gap inserted for an especially large region of heterochromatic sequence\uff1btelomere\uff0ca gap inserted for the telomere\uff1brepeat\uff0can unresolvable repeat\u3002\r\n8. \u5c0f\u7247\u6bb5\u7ed3\u675f\u6216gap\u662f\u5426\u88ab\u8fde\u63a5(component_end or linkage)\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u5982\u679c\u7b2c5\u5217\u662fN\u6216U\uff0c\u5219\u6b64\u5217\u4e00\u822c\u7684\u503c\u4e3ayes\uff0c\u8868\u793a\u6709\u8bc1\u636e\u8868\u660e\u4e34\u8fd1\u76842\u4e2a\u5c0f\u7247\u6bb5\u662f\u76f8\u8fde\u7684\u3002\r\n9. \u5c0f\u7247\u6bb5\u65b9\u5411\u6216gap\u7684\u8fde\u63a5\u65b9\u6cd5(orientation or linkage_evidence)\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u5982\u679c\u7b2c5\u5217\u4e0d\u4e3aN\u6216U\uff0c\u5219\u6b64\u5217\u4e3a\u5c0f\u7247\u6bb5\u7684\u65b9\u5411\u3002\u5176\u5e38\u89c1\u7684\u503c\u4e3a +\u3001-\u6216\uff1f\u3002\r\n&nbsp;&nbsp;&nbsp;&nbsp;\u5982\u679c\u7b2c5\u5217\u662fN\u6216U\uff0c\u5219\u6b64\u5217\u8868\u660e\u4e34\u8fd1\u76842\u4e2a\u5c0f\u7247\u6bb5\u80fd\u8fde\u63a5\u7684\u8bc1\u636e\u7c7b\u578b\u3002\u5176\u7528\u7684\u503c\u662fpaired-ends\uff0c\u8868\u660e\u6210\u5bf9\u7684reads\u5c06\u5c0f\u7247\u6bb5\u8fde\u63a5\u8d77\u6765\u3002\u5176\u5b83\u503c\u6709\uff1ana\uff0c\u7b2c8\u5217\u503c\u4e3ano\u7684\u65f6\u5019\u4f7f\u7528\uff1balign_genus\uff0c\u6bd4\u5bf9\u5230\u540c\u5c5e\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u800c\u8fde\u63a5\uff1balign_xgenus\uff0c\u6bd4\u5bf9\u5230\u5176\u5b83\u5c5e\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u800c\u8fde\u63a5\uff1balign_trnscpt\uff0c\u6bd4\u5bf9\u5230\u540c\u6837\u7269\u79cd\u7684\u8f6c\u5f55\u5b50\u5e8f\u5217\u4e0a\uff1bwithin_clone\uff0cgap\u4e24\u8fb9\u7684\u5e8f\u5217\u6765\u81ea\u4e0e\u540c\u4e00\u4e2aclone\uff0c\u4f46\u662fgap\u6ca1\u6709paired-ends\u8de8\u8d8a\uff0c\u56e0\u6b64\u8fd9\u79cd\u8fde\u63a5\u4e24\u8fb9\u5c0f\u7247\u6bb5\u65e0\u6cd5\u786e\u5b9a\u65b9\u5411\u548c\u987a\u5e8f\uff1bclone_contig\uff0clinkage is provided by a clone contig in the tiling path (TPF)\uff1bmap\uff0c\u6839\u636e\u8fde\u9501\u56fe\uff0c\u5149\u5b66\u56fe\u7b49\u65b9\u6cd5\u786e\u5b9a\u7684\u8fde\u63a5\uff1bstrobe\uff0c\u6839\u636ePacBio\u5e8f\u5217\u5f97\u5230\u7684\u8fde\u63a5\uff1bunspecified\u3002\u5982\u679c\u6709\u591a\u4e2d\u8bc1\u636e\uff0c\u5219\u53ef\u4ee5\u5199\u4e0a\u591a\u79cd\u8bc1\u636e\uff0c\u4e4b\u95f4\u7528\u5206\u53f7\u5206\u5272\u3002\r\n<\/pre>\n<p>\u4f8b\u5b50\uff1a<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/projects\/genome\/assembly\/agp\/scaffold_from_contig_WGS.agp.v2.0.txt\" target=\"_blank\">Scaffold from component (WGS)<\/a><br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/projects\/genome\/assembly\/agp\/chr_from_scaffold_WGS.agp.v2.0.txt\" target=\"_blank\">Chromosome from scaffold (WGS)<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>AGP\u6587\u4ef6\u4e3aNCBI\u6570\u636e\u4e0a\u4f20\u8981\u6c42\u7684\u6807\u51c6\u683c\u5f0f\uff0c\u7528\u6765\u63cf\u8ff0\u5c0f\u7247\u6bb5\u5e8f\u5217\uff08\u6bd4\u5982contig &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2349\">\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":[39,40],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2349"}],"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=2349"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2349\/revisions"}],"predecessor-version":[{"id":2350,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2349\/revisions\/2350"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2349"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2349"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2349"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}