{"id":24283,"date":"2024-01-11T17:01:19","date_gmt":"2024-01-11T09:01:19","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24283"},"modified":"2024-01-11T17:01:21","modified_gmt":"2024-01-11T09:01:21","slug":"motif%e5%af%8c%e9%9b%86%e5%88%86%e6%9e%90%ef%bc%9fhomer%e5%8a%a9%e4%bd%a0%e4%b8%80%e8%87%82%e4%b9%8b%e5%8a%9b%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24283","title":{"rendered":"motif\u5bcc\u96c6\u5206\u6790\uff1fHOMER\u52a9\u4f60\u4e00\u81c2\u4e4b\u529b\uff01"},"content":{"rendered":"

\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u6765\u5566\uff0c\u5927\u5bb6\u8fd8\u8bb0\u5f97motif\u662f\u4ec0\u4e48\u5417\uff1f\u601d\u8003\u4e09\u79d2\u949f\uff0c\u5982\u679c\u4f60\u8fd8\u8bb0\u5f97\u7684\u8bdd\uff0c\u90a3\u5c0f\u679c\u7ed9\u4f60\u5927\u62c7\u54e5\uff01<\/p>\n

\u4e0b\u9762\u5c0f\u679c\u7ed9\u5927\u5bb6\u8be6\u7ec6\u4ecb\u7ecd\u4e0bmotif\uff1amotif\u662f\u6307\u4e00\u6bb5\u5177\u6709\u7279\u5b9a\u529f\u80fd\u6216\u7ed3\u6784\u7684\u5206\u5b50\u5e8f\u5217\u6216\u5143\u7d20\uff0c\u901a\u5e38\u662f\u4fdd\u5b88\u7684\u3001\u91cd\u590d\u7684\u3001\u4e0e\u5176\u4ed6\u5206\u5b50\u76f8\u4e92\u4f5c\u7528\u7684\u3002Motif\u53ef\u4ee5\u5b58\u5728\u4e8eDNA\u3001RNA\u6216\u86cb\u767d\u8d28\u4e2d\uff0c\u4f8b\u5982\u8f6c\u5f55\u56e0\u5b50\u7684\u7ed3\u5408\u4f4d\u70b9\u3001RNA\u9176\u7684\u6d3b\u6027\u4e2d\u5fc3\u3001\u86cb\u767d\u8d28\u7684\u7ed3\u6784\u57df\u7b49\u3002Motif\u53ef\u4ee5\u7528\u5e8f\u5217logo\u56fe\u3001\u4e00\u81f4\u6027\u5e8f\u5217\u6216PFM\u77e9\u9635\u7b49\u65b9\u5f0f\u6765\u8868\u793a\u548c\u5206\u6790\u3002Motif\u7684\u7814\u7a76\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u57fa\u56e0\u8c03\u63a7\u3001\u5206\u5b50\u8fdb\u5316\u3001\u529f\u80fd\u9884\u6d4b\u7b49\u751f\u7269\u5b66\u95ee\u9898\u3002<\/p>\n

\u5e8f\u5217\u57fa\u5e8f\u5728\u57fa\u56e0\u8c03\u63a7\u5206\u6790\u4e2d\u8d8a\u6765\u8d8a\u91cd\u8981\u3002Motif\u5e76\u4e0d\u5c40\u9650\u4e8e\u57fa\u56e0\u7ec4DNA\u5e8f\u5217\u8fd8\u662fRNA\u5e8f\u5217\uff0c\u751a\u81f3\u86cb\u767d\u8d28\u5e8f\u5217\u4e5f\u53ef\u4ee5\u63d0\u53d6\u51fa\u76f8\u5e94\u7684motif\u3002\u5f53\u67d0\u4e00\u4e2a\u5927\u7c7b\u7684\u5e8f\u5217\u4e2d\uff0c\u5927\u91cf\u91cd\u590d\u51fa\u73b0\u76f8\u540c\u7684\u5e8f\u5217\u7ed3\u6784\u7684\u65f6\u5019\uff0c\u5c31\u5b58\u5728\u63a2\u7d22\u5b83\u610f\u4e49\u7684\u4ef7\u503c\u3002\u57fa\u4e8emotif\u5e8f\u5217\u7684\u63d0\u53d6\uff0c\u6211\u4eec\u53ef\u4ee5\u9884\u6d4b\u6f5c\u5728\u7684\u7ed3\u5408\u4f4d\u70b9\u7b49\u7b49\uff0c\u6709\u52a9\u4e8e\u6211\u4eec\u8fdb\u4e00\u6b65\u7406\u89e3\u5404\u751f\u7269\u5b66\u8fc7\u7a0b\u4e2d\u6d89\u53ca\u7684\u751f\u7269\u5b66\u610f\u4e49\u3002<\/p>\n

\u770b\u5230\u8fd9\uff0c\u5927\u5bb6\u662f\u4e0d\u662f\u5bf9motif\u5145\u6ee1\u4e86\u597d\u5947\u5462<\/p>\n

\u5927\u5bb6\u7ecf\u5e38\u770b\u5230\u7684motif\u7684logo\u56fe\u5982\u4e0b\u56fe\u6240\u793a<\/p>\n

<\/p>\n

\u90a3\u600e\u4e48\u53bb\u7406\u89e3motif\u7684logo\u56fe\u5462\uff1f\u5c0f\u679c\u6765\u544a\u8bc9\u5927\u5bb6\uff1amotif\u7684logo\u56fe\u7ecf\u5e38\u7528\u4e8e\u63cf\u8ff0\u5e8f\u5217\u7279\u5f81\uff0c\u5982DNA\u4e2d\u7684\u86cb\u767d\u8d28\u7ed3\u5408\u4f4d\u70b9\u7b49\u3002motif\u7684logo\u56fe\u7531\u6bcf\u4e2a\u4f4d\u7f6e\u7684\u4e00\u5806\u5b57\u6bcd\u7ec4\u6210\u3002\u5b57\u6bcd\u7684\u76f8\u5bf9\u5927\u5c0f\u8868\u793a\u5b83\u4eec\u5728\u5e8f\u5217\u4e2d\u7684\u9891\u7387\u3002\u5b57\u6bcd\u9ad8\u7684\u5c31\u8bf4\u660e\u8be5\u4f4d\u7f6e\u51fa\u73b0\u8fd9\u4e2a\u78b1\u57fa\u7684\u9891\u7387\u66f4\u5927\u3002<\/p>\n

\u90a3\u4e48\u5982\u4f55\u4f7f\u7528homer\u53bb\u9884\u6d4bmotif\u5462\uff1f\u4e0b\u9762\u5c0f\u679c\u5e26\u5927\u5bb6\u4e00\u63a2\u7a76\u7adf\u3002<\/p>\n

\u9996\u5148\u8bf4\u4e00\u4e0b\u7528\u5230\u7684\u8f6f\u4ef6HOMER\uff0cHOMER \u662f\u4e00\u5957\u7528\u4e8eMotif\u67e5\u627e\u548c\u4e8c\u4ee3\u6570\u636e\u5206\u6790\u7684\u5de5\u5177\u3002HOMER \u4e2d\u7684\u5de5\u5177\u662f\u4f7f\u7528Perl \u548cC++\u7f16\u5199\u7684\uff0c\u662fLinux command line based\u3002HOMER \u8fd9\u4e2a\u8f6f\u4ef6\u662f\u4e00\u4e2a\u5927\u6742\u70e9\uff0c\u80fd\u89e3\u51b3\u51e0\u4e4e\u6240\u6709\u7684\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6570\u636e\u7684\u5206\u6790\u3002<\/p>\n

HOMER \u4e00\u4e2a\u5e38\u7528\u7684motif\u5206\u6790\u8f6f\u4ef6\u3002\u5b83\u901a\u8fc7\u6bd4\u8f83\u4e24\u4e2a\u5e8f\u5217\u96c6\uff0c\u5e76\u4f7f\u7528ZOOPS scoring\u548c\u8d85\u51e0\u4f55\u5206\u5e03\uff08\u6216\u8005\u8d1f\u4e8c\u9879\u5206\u5e03\uff09\u8fdb\u884cmotif\u7684\u5bcc\u96c6\u5206\u6790\u3002\u5b83\u4e3b\u8981\u7528\u4e8eChIP-seq\u548cATAC-seq\u548cpromoter\u5206\u6790\uff0c\u4f46\u4e5f\u53ef\u4ee5\u7528\u4e8e\u6838\u9178\u5e8f\u5217\u7684motif\u5206\u6790\u95ee\u9898\u3002<\/p>\n

HOMER\u8f6f\u4ef6\u53ef\u4ee5\u8fdb\u884c\u591a\u79cd\u7c7b\u578b\u7684motif\u5206\u6790\uff0c\u5982 promoter motif analysis \uff0c\u57fa\u56e0\u7ec4\u4f4d\u7f6emotif\u5206\u6790(ChIP-seq\u5206\u6790\u4e2d\u7684motif\u5206\u6790)\uff0c\u5229\u7528\u81ea\u5b9a\u4e49\u7684fasta\u6587\u4ef6\u8fdb\u884cmotif\u5206\u6790\uff0cRNA\u5e8f\u5217\u7684motif\u5206\u6790\uff08\u5206\u6790CLIP-seq\u6570\u636e\u4e2d\u7684RNA binding elements\uff09\u3002<\/p>\n

\u8fd9\u662fHOMER\u8f6f\u4ef6\u7684\u5b98\u7f51\u5730\u5740\uff1a<\/p>\n

http:\/\/homer.ucsd.edu\/homer\/ngs\/peakMotifs.html<\/a>\uff0c\u5927\u5bb6\u4e00\u5b9a\u8981\u517b\u6210\u591a\u770b\u5b98\u65b9\u6587\u6863\u7684\u597d\u4e60\u60ef\u55f7<\/p>\n

HOMER\u7684\u5b89\u88c5\u53ef\u4ee5\u4f7f\u7528conda\u6765\u5b8c\u6210\uff1a<\/p>\n

conda install -c bioconda homer<\/strong><\/p>\n

\u4e0b\u9762\u9700\u8981configureHomer.pl\u5b8c\u6210Homer\u8f6f\u4ef6\u7684\u914d\u7f6e\uff1a<\/p>\n

    \n
  1. \u5148\u4e0b\u8f7dconfigureHomer.pl\uff1a<\/li>\n<\/ol>\n

    wget\u00a0http:\/\/homer.ucsd.edu\/homer\/configureHomer.pl<\/a><\/p>\n

      \n
    1. \u4f7f\u7528configureHomer.pl\u914d\u7f6eHomer\uff08\u5c0f\u4f19\u4f34\u4eec\u6ce8\u610f\u6587\u4ef6\u8def\u5f84\u95ee\u9898\u55f7\uff09<\/li>\n<\/ol>\n

      perl\u00a0configureHomer.pl \u00a0[options]<\/p>\n

      \u5927\u5bb6\u53ef\u4ee5\u4f7f\u7528configureHomer.pl\u6765\u914d\u7f6eHomer\uff0c\u4f8b\u5982\u4e0b\u8f7d\u4eba\u7c7b\uff0c\u5c0f\u9f20\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u7b49\uff0c\u4eba\u548c\u5c0f\u9f20\u7684\u7814\u7a76\u5c45\u591a\uff0c\u8fd9\u91cc\u53ea\u4ee5\u8fd9\u4e24\u8005\u4e3e\u4f8b<\/p>\n

      # \u4e0b\u8f7d hg19 \u4eba\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\uff0c\u5c06hg19\u66ff\u6362\u4e3amm10\u53ef\u4e0b\u8f7dmm10 \u5c0f\u9f20\u7684\u53c2\u8003\u57fa\u56e0\u7ec4<\/p>\n

      perl configureHomer.pl -install hg19<\/p>\n

      \u4e0d\u8fc7\u8fd9\u91cc\u5c0f\u679c\u7814\u7a76\u7684\u662f\u975e\u6a21\u5f0f\u751f\u7269\uff0c\u90a3\u4e48\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u4e00\u8d77\u7528\u53ef\u7231\u7684\u5bb6\u8695\u6765\u5b66\u4e60HOMER\u8f6f\u4ef6\u5427<\/p>\n

      \u9996\u5148\u5c0f\u679c\u770b\u7f51\u4e0a\u5c0f\u4f19\u4f34\u8bf4\u4f7f\u7528\u672c\u5730\u7684\u53c2\u770b\u57fa\u56e0\u7ec4\u76f4\u63a5\u547d\u4ee4\u884c\u4f7f\u7528\u5c31\u884c\uff0c\u53ef\u628a\u5c0f\u679c\u5bb3\u82e6\u4e86\uff0c\u4e00\u76f4error\uff01\u4e0d\u8fc7\u4e0d\u614c\uff0c\u5c0f\u679cdebug\u662f\u6700\u5f3a\u7684\uff0c\u5c0f\u679c\u53c8\u67e5\u5230\u662f\u56e0\u4e3a\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u95ee\u9898\uff0c\u770b\u4e86\u770bhomer\u7684\u7248\u672c\uff1a<\/p>\n

      <\/p>\n

      \u5c0f\u679c\u901a\u8fc7\u67e5\u9605\u5b98\u7f51\u53d1\u73b0\u4ecehomer v4.4 \u5f00\u59cb\u5c31\u53ef\u4ee5\u81ea\u5b9a\u4e49homer\u4e86\uff0c\u6240\u4ee5\u6211\u4eec\u9700\u8981\u4f7f\u7528loadGenome.pl\u6216loadPromoters.pl\u547d\u4ee4\u521b\u5efa\u81ea\u5df1\u7684\u57fa\u56e0\u7ec4\u548c\u542f\u52a8\u5b50 FASTA \u6216\u6ce8\u91ca\u6587\u4ef6<\/p>\n

      \u67e5\u9605\u5e2e\u52a9\u6587\u6863\u53d1\u73b0\uff1a<\/p>\n

      Required Parameters:<\/p>\n

      -name <genome name> (i.e. hg19, tair10, etc.)<\/p>\n

      -fasta <genome fasta file> (Single genome sequence, preferrabley soft masked, unzipped)<\/p>\n

      -gtf <gene annotation file> (Transcript annotation in gtf format, -gff\/-gff3 to use them)<\/p>\n

      -org <organism name, ok to use ‘null’><\/p>\n

      \u6240\u4ee5\u6211\u4eec\u9700\u8981\u53c2\u8003\u57fa\u56e0\u7ec4fasta\u6587\u4ef6\u548cgtf\u6587\u4ef6<\/p>\n

      \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u4ee3\u7801\uff1a<\/p>\n

      loadGenome.pl -gtf test.gtf -name test -fasta test_assembly.fa -org null<\/p>\n

      \u4e0b\u9762\u5c31\u662f\u9884\u6d4bmotif\u7684\u8fc7\u7a0b\u4e86\uff0c\u4ee5CHIP-seq\u6d41\u7a0b\u4e3a\u4f8b\uff0c\u8f93\u5165\u6587\u4ef6\u53ef\u4ee5\u662fMACS2\u8f6f\u4ef6callpeak\u7684bed\u6587\u4ef6(\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528)\u6216\u8005\u662fHOMER\u8f6f\u4ef6\u6307\u5b9a\u7684peak\u6587\u4ef6\u683c\u5f0f\u3002peak\u6587\u4ef6\u683c\u5f0f\uff1a\u4f7f\u7528Tab\u5206\u9694\uff0c\u5171\u4e94\u5217\uff0c\u5206\u522b\u662f peak ID , chr , start , end ,strand<\/p>\n

      \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u4ee3\u7801\uff1a<\/p>\n

      findMotifsGenome.pl test.bed test sample_motif_dir -len 8,10,12<\/p>\n

      \u53c2\u6570\u7684\u89e3\u91ca\u5982\u4e0b\uff1a<\/p>\n

      test.bed \uff1a bed\u683c\u5f0f\u6587\u4ef6<\/p>\n

      test \uff1a \u81ea\u5b9a\u4e49\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\uff08loadGenome.pl\u547d\u4ee4\u4e2d\u7684name\u53c2\u6570\uff09<\/p>\n

      sample_motif_dir \uff1a \u8f93\u51fa\u6587\u4ef6\u5939<\/p>\n

      -len \uff1amotif\u7684\u957f\u5ea6\uff0c\u9ed8\u8ba48\uff0c10\uff0c12\uff0c\u8d8a\u5927\u8d8a\u6d88\u8017\u8ba1\u7b97\u8d44\u6e90<\/p>\n

      HOMER\u7684\u8f93\u51fa\u7ed3\u679c\u4e2d\u6709\u540d\u4e3ahomerResults.html\u7684\u7f51\u9875\u6587\u4ef6\uff0c\u5728\u91cc\u9762\u53ef\u4ee5\u8be6\u7ec6\u7684\u770b\u5230motif\u7684\u7ed3\u679c\uff0c\u4e0b\u9762\u662f\u5c0f\u679c\u7684\u7ed3\u679c<\/p>\n

      <\/p>\n

      \u8f93\u51fa\u7ed3\u679c\u6309\u7167p-value\u6392\u5e8f\uff0c\u6700\u540e\u4e00\u5217\u662f\u4e00\u4e2a\u94fe\u63a5\u5230motif\u6587\u4ef6\u7684\u8d85\u94fe\u63a5\uff0c\u53ef\u4ee5\u4ece\u8fd9\u4e2a\u6587\u4ef6\u4e2d\u627e\u5230\u5305\u542b\u6b64motif\u7684\u5176\u4ed6\u5e8f\u5217\u3002\u5728Best Match\/Details \u5217\u4e2d\uff0cHOMER\u5c55\u793a\u4e0edenovo motif\u6700\u5339\u914d\u7684\u5df2\u77e5motif\u3002<\/p>\n

      \u4eca\u5929\u7684\u5173\u4e8ehomer\u9884\u6d4bmotif\u7684\u5b66\u4e60\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\uff0c\u6709\u611f\u89c9\u751f\u4fe1\u5206\u6790\u590d\u6742\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528\u6211\u4eec\u7684\u751f\u4fe1\u5c0f\u5de5\u5177\u54e6\uff0c\u94fe\u63a5\u5728\u8fd9\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/a>\uff0c\u6211\u4eec\u660e\u5929\u89c1\u54af~<\/p>\n","protected":false},"excerpt":{"rendered":"

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