{"id":1079,"date":"2017-07-17T09:18:55","date_gmt":"2017-07-17T01:18:55","guid":{"rendered":"https:\/\/lsl.sinica.edu.tw\/Blog\/?p=1079"},"modified":"2017-08-17T11:40:51","modified_gmt":"2017-08-17T03:40:51","slug":"cd-hit","status":"publish","type":"post","link":"https:\/\/lsl.sinica.edu.tw\/Blog\/2017\/07\/cd-hit\/","title":{"rendered":"\u597d\u7528\u7684\u5e8f\u5217\u6bd4\u5c0d\u8207\u5206\u7fa4\u5de5\u5177\uff1aCD-HIT"},"content":{"rendered":"<p>&nbsp;<\/p>\n<p><a href=\"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-content\/uploads\/2017\/06\/20170717.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-1086\" src=\"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-content\/uploads\/2017\/06\/20170717-768x1024.png\" alt=\"20170717\" width=\"580\" height=\"773\" \/><\/a><\/p>\n<p><!--more--><\/p>\n<h3>CD-HIT\u662f\u4e00\u500b\u61c9\u7528\u5ee3\u6cdb\u7684\u5e8f\u5217\u6bd4\u5c0d\u5206\u7fa4\u8edf\u9ad4\uff0c\u5b83\u53ef\u4ee5\u5e6b\u4f60\u627e\u5230\u5177\u6709\u4ee3\u8868\u6027\u7684\u5e8f\u5217\uff0c\u5728\u5408\u7406\u6642\u9593\u5167\u8655\u7406\u5de8\u91cf\u7684\u5e8f\u5217\u8cc7\u6599\uff0c\u5927\u5927\u964d\u4f4e\u4f60\u64c1\u6709\u8cc7\u6599\u7684\u8907\u96dc\u5ea6\uff0c\u6e1b\u5c11\u5f8c\u7e8c\u8a08\u7b97\u9700\u6c42\u3002\u525b\u63a8\u51fa\u6642CD-HIT\u8457\u91cd\u65bc\u91dd\u5c0d\u86cb\u767d\u8cea\u5e8f\u5217\u7684\u5206\u7fa4\uff0c\u76ee\u524d\u5c0d\u65bcDNA\u5e8f\u5217\u751a\u81f3\u65bc\u5c0d\u8655\u7406\u6b21\u4e16\u4ee3\u5b9a\u5e8f\u7684\u539f\u59cb\u77ed\u5e8f\u5217\u4e5f\u6709\u76f8\u5c0d\u61c9\u7684\u7a0b\u5f0f\u53ef\u4f9b\u4f7f\u7528\uff0c\u4f7f\u5b83\u7684\u61c9\u7528\u66f4\u52a0\u5ee3\u6cdb\u3002<\/h3>\n<h3><\/h3>\n<h3>\u8209\u4f8b\u4f86\u8aaa\uff0c\u5047\u4f7f\u4f60\u4f7f\u7528\u4e86\u5e8f\u5217\u7d44\u88dd\u8edf\u9ad4\u4f86\u8655\u7406\u8f49\u9304\u9ad4\u8cc7\u6599\uff0c\u5f97\u5230\u4e86\u6578\u4ee5\u842c\u8a08\u7684transcripts\uff0c\u4ed4\u7d30\u6aa2\u67e5\u5f8c\u767c\u73fe\u9019\u4e9btranscripts\u4e2d\u5176\u5be6\u5f7c\u6b64\u9593\u6709\u76f8\u7576\u7a0b\u5ea6\u7684\u96f7\u540c\uff1b\u6b64\u60c5\u6cc1\u56fa\u7136\u6709\u53ef\u80fd\u56e0\u70ba\u751f\u7269\u9ad4\u4e2d\u539f\u672c\u5373\u5b58\u5728\u4e0d\u540c\u7684transcript 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href=\"https:\/\/github.com\/weizhongli\/cdhit\/releases\">https:\/\/github.com\/weizhongli\/cdhit\/releases<\/a>\u4e0b\u8f09\u6700\u65b0\u7248\u672c\u7684CD-HIT\uff0c\u5728LINUX\u7cfb\u7d71\u4e0b\u89e3\u58d3\u7e2e\u5f8c\uff0c\u4f9d\u7167README\u7684\u7c21\u55ae\u6307\u793a\u64cd\u4f5c\u5b89\u88dd\u4f7f\u7528\u3002<\/h3>\n<h3><\/h3>\n<h3>CD-HIT\u63d0\u4f9b\u4e86\u540c\u4e00\u7d44\u5167\u5e8f\u5217\u6bd4\u8f03\uff0c\u8207\u5169\u7d44\u9593\u5e8f\u5217\u6bd4\u8f03\u7684\u529f\u80fd\u3002\u7576\u6211\u5011\u5c0d\u4e00\u7d44\u86cb\u767d\u8cea(\u6216DNA)\u5e8f\u5217\u505a\u76f8\u4f3c\u5ea6\u5206\u7fa4\u6642\uff0c\u53ef\u4f7f\u7528\u5957\u7d44\u5167\u7684CD-HIT\u529f\u80fd(\u6216CD-HIT-EST)\uff0c\u4e26\u81ea\u5df1\u8a2d\u5b9a\u53c3\u6578\u4ee5\u5b9a\u7fa9\u4f60\u8981\u7684\u76f8\u4f3c\u7a0b\u5ea6\u3002\u540c\u6a23\u7684\uff0c\u82e5\u60f3\u8981\u6bd4\u5c0d\u5169\u7d44\u86cb\u767d\u8cea(\u6216DNA)\u5e8f\u5217\u662f\u5426\u76f8\u4f3c\u6642\uff0c\u6539\u70ba\u4f7f\u7528CD-HIT-2D(\u6216CD-HIT-EST-2D)\u3002<\/h3>\n<h3><\/h3>\n<h3>\u6307\u4ee4\u7bc4\u4f8b\uff1a<\/h3>\n<h3><a href=\"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-content\/uploads\/2017\/06\/CD-HIT1.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-1081\" src=\"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-content\/uploads\/2017\/06\/CD-HIT1.png\" alt=\"CD-HIT1\" width=\"643\" height=\"23\" \/><\/a><\/h3>\n<h3>\u9019\u88e1\u5217\u51fa\u5e7e\u500b\u6bd4\u8f03\u5e38\u7528\u7684\u53c3\u6578\uff1a<\/h3>\n<h3>-i : \u8f38\u5165\u6a94\u6848\u540d\u7a31\uff0c\u4f8b\u5982my_input.fa<\/h3>\n<h3>-o : \u8f38\u51fa\u540d\u7a31\uff0c\u4f8b\u5982my_output90<\/h3>\n<h3>-c : \u76f8\u4f3c\u5ea6\u8a2d\u5b9a\uff0c\u4f8b\u59820.9 = 90%\uff0c\u5373\u76f8\u4f3c\u5ea6\u9ad8\u65bc90%\u7684\u5e8f\u5217\u6703\u88ab\u7576\u6210\u540c\u4e00\u7fa4\u96c6\u3002<\/h3>\n<h3>-n : \u6846\u67b6\u9577\u5ea6\uff0c\u4e0d\u540c\u7684\u76f8\u4f3c\u5ea6\u6709\u5176\u5efa\u8b70\u7684n\u503c\u8a2d\u5b9a\uff0c\u4f8b\u598290%\u6642\u5efa\u8b70n =5\u3002<\/h3>\n<h3>-M : 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src=\"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-content\/uploads\/2017\/06\/CD-HIT2.png\" alt=\"CD-HIT2\" width=\"574\" height=\"112\" \/><\/a><\/h3>\n<h3>\u8f38\u51fa\u7d50\u679c\u540c\u6642\u4e5f\u5305\u542b\u4e00\u500bfasta\u6a94\u6848(\u4f8b\u5982my_output90.fa)\uff0c\u6a94\u6848\u4e2d\u5217\u51fa\u6240\u6709\u7fa4\u96c6\u7684\u4ee3\u8868\u5e8f\u5217(\u4e5f\u5c31\u662f\u5f8c\u9762\u9644\u8a3b*\u7684\u90a3\u4e9b)\uff0c\u4f7f\u7528\u8005\u53ef\u76f4\u63a5\u53d6\u6b64\u6a94\u505a\u5f8c\u7e8c\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u3002<\/h3>\n<h3><\/h3>\n<h3>\u53e6\u5916\u56e0\u61c9\u6b21\u4e16\u4ee3\u5b9a\u5e8f\u7684\u767c\u5c55\uff0c\u65b0\u7248\u672c\u7684CD-HIT\u8207\u6642\u4ff1\u9032\uff0c\u9678\u7e8c\u63a8\u51faCD-HIT-DUP\u8207CD-HIT-454\u7b49\u529f\u80fd\u7528\u4ee5\u8655\u7406\u4f86\u81eaIllumina\u6216454\u5e73\u53f0\u7684\u5b9a\u5e8f\u7d50\u679c\u539f\u59cb\u5e8f\u5217\uff0c\u800c\u539f\u672c\u7684CD-HIT-EST\u8207CD-HIT-EST-2D\u529f\u80fd\u4e5f\u53ef\u7528\u4f86\u8655\u7406paired-end\u7684\u539f\u59cb\u5e8f\u5217\u8cc7\u6599\u4e86\uff01<\/h3>\n<h3><\/h3>\n<h3>(\u53ef\u53c3\u8003\u5b98\u65b9\u7db2\u9801\uff1a<a href=\"http:\/\/weizhongli-lab.org\/cd-hit\/\">http:\/\/weizhongli-lab.org\/cd-hit\/<\/a>)<\/h3>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<h1 style=\"text-align: center;\"><span style=\"color: #0000ff;\">\u611f\u8b1d TIGP \u7684 chunyic \u540c\u5b78\u63d0\u4f9b\u4ee5\u4e0a\u8cc7\u6599<\/span><\/h1>\n<p>&nbsp;<\/p>\n<div class=\"pld-like-dislike-wrap pld-template-1\">\r\n    <div class=\"pld-like-wrap  pld-common-wrap\">\r\n    <a href=\"javascript:void(0)\" class=\"pld-like-trigger pld-like-dislike-trigger  \" title=\"\u8b9a\" data-post-id=\"1079\" data-trigger-type=\"like\" data-restriction=\"ip\" data-already-liked=\"0\">\r\n                        <i class=\"fas fa-thumbs-up\"><\/i>\r\n                <\/a>\r\n    <span class=\"pld-like-count-wrap pld-count-wrap\">0    <\/span>\r\n<\/div><\/div>","protected":false},"excerpt":{"rendered":"<p>&nbsp; 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