{"id":1323,"date":"2013-05-22T22:22:12","date_gmt":"2013-05-22T14:22:12","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1323"},"modified":"2013-10-26T14:09:46","modified_gmt":"2013-10-26T06:09:46","slug":"gff3%e6%a0%bc%e5%bc%8f","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1323","title":{"rendered":"GFF3\u683c\u5f0f"},"content":{"rendered":"

GFF3\u7684\u5b98\u65b9\u4ecb\u7ecd\uff1aGeneric Feature Format Version 3 \uff08GFF3\uff09<\/a><\/p>\n

1. GFF3\u6587\u4ef6\u683c\u5f0f\u63cf\u8ff0<\/h1>\n

GFF3\u683c\u5f0f\u6587\u4ef6\u4e3a\u6587\u672c\u6587\u4ef6\uff0c\u5206\u4e3a9\u5217\uff0c\u4ee5TAB\u5206\u5f00\u3002\u63a7\u5236\u7b26\u4f7f\u7528 RFC 3986 Percent-Encoding<\/a> \u7f16\u7801\u3002\u6bd4\u5982\uff1a%20 \u4ee3\u8868\u7740ASCII\u7684\u7a7a\u683c\u3002<\/p>\n

9\u5217\u6587\u4ef6\u4f9d\u6b21\u662f\uff1a<\/p>\n

1. seqid\uff1a\u53c2\u8003\u5e8f\u5217\u7684id\u3002\u8be5id\u7684\u53d6\u540d\u4e0d\u80fd\u4ee5’>’\u5f00\u5934\uff0c\u4e0d\u80fd\u5305\u542b\u7a7a\u683c\u3002<\/p>\n

2. source \uff1a\u6ce8\u91ca\u7684\u6765\u6e90\u3002\u5982\u679c\u672a\u77e5\uff0c\u5219\u7528\u70b9\uff08.\uff09\u4ee3\u66ff\u3002\u4e00\u822c\u6307\u660e\u4ea7\u751f\u6b64gff3\u6587\u4ef6\u7684\u8f6f\u4ef6\u6216\u65b9\u6cd5\u3002<\/p>\n

3. type \uff1a\u5c5e\u6027\u7684\u7c7b\u578b\u3002\u5efa\u8bae\u4f7f\u7528\u7b26\u5408SO\u60ef\u4f8b\u7684\u540d\u79f0\uff08sequence ontology\uff0c\u53c2\u770b[[Sequence Ontology Project]]) ,\u5982gene\uff0crepeat_region\uff0cexon\uff0cCDS\u7b49\u3002<\/p>\n

4. start position \uff1a\u5c5e\u6027\u5bf9\u5e94\u7247\u6bb5\u7684\u8d77\u70b9\u3002\u4ece1\u5f00\u59cb\u8ba1\u6570\u3002<\/p>\n

5. end position \uff1a\u5c5e\u6027\u5bf9\u5e94\u7247\u6bb5\u7684\u7ec8\u70b9\u3002\u4e00\u822c\u6bd4\u8d77\u70b9\u7684\u6570\u503c\u8981\u5927\u3002<\/p>\n

6. score \uff1a\u5f97\u5206\uff0c\u5bf9\u4e8e\u4e00\u4e9b\u53ef\u4ee5\u91cf\u5316\u7684\u5c5e\u6027\uff0c\u53ef\u4ee5\u5728\u6b64\u8bbe\u7f6e\u4e00\u4e2a\u6570\u503c\u4ee5\u8868\u793a\u7a0b\u5ea6\u7684\u4e0d\u540c\u3002\u5982\u679c\u4e3a\u7a7a\uff0c\u7528\u70b9\uff08.\uff09\u4ee3\u66ff\u3002<\/p>\n

7. strand \uff1a\u201c\uff0b\u201d\u8868\u793a\u6b63\u94fe\uff0c\u201c\uff0d\u201d\u8868\u793a\u8d1f\u94fe\uff0c\u201c.\u201d\u8868\u793a\u4e0d\u9700\u8981\u6307\u5b9a\u6b63\u8d1f\u94fe\u3002<\/p>\n

8. phase \uff1a\u6b65\u8fdb\u3002\u5bf9\u4e8e\u7f16\u7801\u86cb\u767d\u8d28\u7684CDS\u6765\u8bf4\uff0c\u672c\u5217\u6307\u5b9a\u4e0b\u4e00\u4e2a\u5bc6\u7801\u5b50\u5f00\u59cb\u7684\u4f4d\u7f6e\u3002\u53ef\u4ee5\u662f0\uff0c1\u62162\uff0c\u8868\u793a\u5230\u8fbe\u4e0b\u4e00\u4e2a\u5bc6\u7801\u5b50\u9700\u8981\u8df3\u8fc7\u7684\u78b1\u57fa\u4e2a\u6570\u3002
\n\u5bf9\u4e8e\u5176\u5b83\u5c5e\u6027\uff0c\u5219\u7528\u70b9\uff08.\uff09\u4ee3\u66ff\u3002<\/p>\n

9. attributes \uff1a\u5c5e\u6027
\n\u4e00\u4e2a\u5305\u542b\u4f17\u591a\u5c5e\u6027\u7684\u5217\u8868\u3002\u683c\u5f0f\u4e3a\u201c\u6807\u7b7e\uff1d\u503c\u201d\uff08tag=value\uff09\u3002\u4e0d\u540c\u5c5e\u6027\u4e4b\u95f4\u4ee5\u5206\u53f7\u76f8\u9694\u3002\u53ef\u4ee5\u5b58\u5728\u7a7a\u683c\uff0c\u4e0d\u8fc7\u82e5\u6709\u201c,=;\u201d\u5219\u7528URL\u8f6c\u4e49\uff08URL escaping rule\uff09\uff0c\u540c\u65f6TAB\u4e5f\u9700\u8981\u8f6c\u6362\u4e3a\u201c%09\u201d\u8868\u793a\u3002\u6240\u6709\u4ee5\u5927\u5199\u5b57\u5e55\u5f00\u5934\u7684\u6807\u7b7e\u88ab\u4fdd\u7559\uff0c\u7528\u4e8e\u5927\u4f17\u8ba4\u53ef\u7684\u7528\u9014\uff0c\u800c\u4ee5\u5c0f\u5199\u5b57\u6bcd\u5f00\u5934\u7684\u6807\u7b7e\u5219\u6839\u636e\u81ea\u5df1\u5b89\u6392\u968f\u610f\u5e94\u7528\u3002
\n\u5e38\u7528\u7684\u6807\u7b7e\u6709\uff1a
\nID
\nFeature\u7684\u6807\u8bc6\u3002\u8be5ID\u5177\u6709\u552f\u4e00\u6027\u3002
\nName
\nFeature\u7684\u5c55\u793a\u540d\u79f0\u3002Name\u7684\u503c\u5728\u53ef\u89c6\u5316\u7684\u65f6\u5019\u5f97\u5230\u5c55\u793a\u3002\u56e0\u6b64\uff0cName\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u5c55\u793a\u7684\u9700\u8981\u968f\u610f\u53d6\u503c\u3002
\nAlias
\nFeature\u7684\u7b2c2\u4e2aName\u3002
\nParent
\n\u6307\u660efeature\u6240\u4ece\u5c5e\u7684\u4e0a\u4e00\u7ea7ID\u3002\u7528\u4e8e\u5c06exons\u805a\u96c6\u6210transcript\uff0c\u5c06transripts\u805a\u96c6\u6210gene\u3002
\nTarget
\n\u6307\u660e\u6bd4\u5bf9\u7684\u76ee\u6807\u533a\u57df\uff0c\u4e00\u822c\u7528\u4e8e\u8868\u660e\u5e8f\u5217\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u683c\u5f0f\u4e3a”target_id start end [strand]”,\u5176\u4e2dstrand\u662f\u53ef\u9009\u7684(“+”\u6216”-“), target_id\u4e2d\u5982\u679c\u5305\u542b\u7a7a\u683c\uff0c\u5219\u8981\u8f6c\u6362\u6210’%20’\u3002
\nGap
\n\u6bd4\u5bf9\u7ed3\u679c\u7684gap\u4fe1\u606f\uff0c\u548cTarget\u4e00\u8d77\uff0c\u7528\u4e8e\u8868\u660e\u5e8f\u5217\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002
\nNote
\n\u6587\u672c\u63cf\u8ff0
\nIs_circular
\n\u8868\u660efeatrue\u662f\u5426\u4e3a\u73af\u5316\u7684\u3002\u7528\u4e8e\u73af\u72b6\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002<\/p>\n

\u540c\u4e00\u4e2atag\u5982\u679c\u6709\u591a\u4e2a\u503c\uff0c\u5219\u591a\u4e2a\u503c\u4e4b\u95f4\u4f7f\u7528\u9017\u53f7\u9694\u5f00\uff0c\u6bd4\u5982\uff1a
\nParent=AF2312,AB2812,abc-3
\nAlias=M19211,gna-12,GAMMA-GLOBULIN
\n\u80fd\u591f\u4f7f\u7528\u591a\u4e2a\u503c\u7684tag\u6709\uff1aParent, Alias, Note, Dbxref and Ontology_term\u3002<\/p>\n

2. GFF3\u6587\u4ef6\u68c0\u6d4b<\/h1>\n

\u68c0\u9a8cGFF3\u683c\u5f0f\u6587\u4ef6\uff1a GFF3 Validator<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

GFF3\u7684\u5b98\u65b9\u4ecb\u7ecd\uff1aGeneric Feature Format Version … \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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1323"}],"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=1323"}],"version-history":[{"count":4,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1323\/revisions"}],"predecessor-version":[{"id":1976,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1323\/revisions\/1976"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1323"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1323"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1323"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}