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style=\"box-sizing: border-box;max-width: 100%;\">\n<section>\n<section style=\"box-sizing: border-box;max-width: 100%;\">\n<section>\n<section style=\"box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"box-sizing: border-box;\">\n<section style=\"line-height: 1.8;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"box-sizing: border-box;\">\n<section style=\"box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;font-size: 16px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\">\n<section style=\"padding-right: 5px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;line-height: 0;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"transform: perspective(0px);transform-style: flat;box-sizing: border-box;\">\n<section style=\"text-align: center;transform: rotateY(180deg);line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 21px;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8823529\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/2_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/3_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/4_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_svg\/oYwP0cFmRU1GD1tysLsmLNIM78AS2IutDaNX2fF75dw9icJ9mn1Av9PtibYjXJzzhvZiaric9mJroULZzpxvu1CNECJiap0wuxqRI\/640?wx_fmt=svg'''\" data-type=\"svg\" data-w=\"170\" style=\"height: 18.4896px;vertical-align: middle;width: 20.9896px;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding: 3px 20px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;background-color: rgb(255, 128, 52);box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\">\n<p><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">Homer<span style=\"font-family:\u5b8b\u4f53;\">\u662f\u5e72\u561b\u7684\uff1f<\/span><\/span><\/strong><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"box-sizing: border-box;\">\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">HOMER<span style=\"font-family:\u5b8b\u4f53;\">\u662f\u4e00\u5957\u57fa\u4e8e <\/span><span style=\"font-family:Times New Roman;\">C++ <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u548c <\/span><span style=\"font-family:Times New Roman;\">Perl <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u8bed\u8a00\u7684\u7528\u4e8e <\/span><span style=\"font-family:Times New Roman;\">motif <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u67e5\u627e\u548c\u4e8c\u4ee3\u6570\u636e\u5206\u6790\u7684\u5de5\u5177\uff0c\u4e00\u822c\u9700\u8981\u4e24\u4e2a\u5e8f\u5217\u4f5c\u4e3a\u53c2\u6570\uff1a<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:Times New Roman;\">\u25cf <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u53c2\u8003\u5e8f\u5217\uff1a<\/span><span style=\"font-family:Times New Roman;\">hg19<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3001<\/span><span style=\"font-family:Times New Roman;\">mm10 <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u7b49\u57fa\u56e0\u7ec4\u5e8f\u5217\u3001<\/span><span style=\"font-family:Times New Roman;\">promoter <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217\u3001\u81ea\u5b9a\u4e49\u7684 <\/span><span style=\"font-family:Times New Roman;\">FASTA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:Times New Roman;\">\u25cf <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6240\u8981\u5206\u6790\u7684\u5e8f\u5217\uff1a<\/span><span style=\"font-family:Times New Roman;\">DNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6216 <\/span><span style=\"font-family:Times New Roman;\">RNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">HOMER <span style=\"font-family:\u5b8b\u4f53;\">\u9002\u7528\u4e8e\u5728\u5927\u89c4\u6a21\u6570\u636e\u4e2d\u5bfb\u627e <\/span><span style=\"font-family:Times New Roman;\">DNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6216 <\/span><span style=\"font-family:Times New Roman;\">RNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217\u7684 <\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002<\/span><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;font-size: 16px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\">\n<section style=\"padding-right: 5px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;line-height: 0;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"transform: perspective(0px);transform-style: flat;box-sizing: border-box;\">\n<section style=\"text-align: center;transform: rotateY(180deg);line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 21px;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8823529\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/2_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/3_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/4_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_svg\/oYwP0cFmRU1GD1tysLsmLNIM78AS2IutDaNX2fF75dw9icJ9mn1Av9PtibYjXJzzhvZiaric9mJroULZzpxvu1CNECJiap0wuxqRI\/640?wx_fmt=svg'''\" data-type=\"svg\" data-w=\"170\" style=\"height: 18.4896px;vertical-align: middle;width: 20.9896px;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding: 3px 20px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;background-color: rgb(255, 128, 52);box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\">\n<p><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"> <span style=\"font-family:\u5b8b\u4f53;\">\u90a3\u4ec0\u4e48\u662f <\/span><span style=\"font-family:Times New Roman;\">motif <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5462\uff1f<\/span><\/span><\/strong><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"font-size: 16px;box-sizing: border-box;\">\n<p style=\"margin-right: 0pt;margin-left: 0pt;\"><br \/><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">motif<span style=\"font-family:\u5b8b\u4f53;\">\uff1a\u53cd\u590d\u51fa\u73b0\u7684\u6a21\u5f0f\uff0c\u5373\u4e00\u79cd\u7279\u5f81\u5e8f\u5217\uff0c\u6bd4\u5982 <\/span><span style=\"font-family:Times New Roman;\">sequence motif, structure motif, network motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002\u5b83\u6709\u6216\u8005\u53ef\u80fd\u6709\u4e00\u5b9a\u7684\u751f\u7269\u5b66\u529f\u80fd\u3002<\/span><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;font-size: 16px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\">\n<section style=\"padding-right: 5px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;line-height: 0;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"transform: perspective(0px);transform-style: flat;box-sizing: border-box;\">\n<section style=\"text-align: center;transform: rotateY(180deg);line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 21px;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8823529\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/2_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/3_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/4_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_svg\/oYwP0cFmRU1GD1tysLsmLNIM78AS2IutDaNX2fF75dw9icJ9mn1Av9PtibYjXJzzhvZiaric9mJroULZzpxvu1CNECJiap0wuxqRI\/640?wx_fmt=svg'''\" data-type=\"svg\" data-w=\"170\" style=\"height: 18.4896px;vertical-align: middle;width: 20.9896px;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding: 3px 20px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;background-color: rgb(255, 128, 52);box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\">\n<p><strong><span style=\"font-size: 12pt;font-family: \u5b8b\u4f53;\">\u5177\u4f53\u5206\u6790\u6b65\u9aa4<\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.1 linux<span style=\"font-family: \u5b8b\u4f53;\">\u914d\u7f6e\u65b0\u73af\u5883<\/span><\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">conda create -n work puthon=3.8<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">conda activate work<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.2 homer<span style=\"font-family: \u5b8b\u4f53;\">\u5b89\u88c5<\/span><\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">conda install -c bioconda homer<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">##<span style=\"font-family:\u5b8b\u4f53;\">\u4e0b\u8f7d<\/span><span style=\"font-family:Times New Roman;\">configureHomer.pl<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">wget http:\/\/homer.ucsd.edu\/homer\/configureHomer.pl<\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">##<span style=\"font-family:\u5b8b\u4f53;\">\u4f7f\u7528<\/span><span style=\"font-family:Times New Roman;\">configureHomer.pl<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u914d\u7f6e<\/span><span style=\"font-family:Times New Roman;\">Homer<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">perl configureHomer.pl -install <o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">perl configureHomer.pl -install mm10<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3 homer<span style=\"font-family: \u5b8b\u4f53;\">\u5206\u6790<\/span><\/span><\/strong><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.1 Analyzing lists of genes with promoter motif analysis (findMotifs.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">############<span style=\"font-family:\u5b8b\u4f53;\">\u5bfb\u627e\u57fa\u56e0\u5217\u8868\u542f\u52a8\u5b50\u4e0a\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5bcc\u96c6<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">findMotifs.pl 3v3135F15Q001gene.txt mouse \/public\/home\/wjiang\/zhan\/work\/homer\/testdata -len 10<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.2 Analyzing genomic positions(findMotifsGenome.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">####<span style=\"font-family:\u5b8b\u4f53;\">\u8f93\u5165\u4e3a<\/span><span style=\"font-family:Times New Roman;\">bed<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6587\u4ef6\uff0c\u4e3b\u8981\u662f<\/span><span style=\"font-family:Times New Roman;\">chip-seq<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6570\u636e\u901a\u8fc7<\/span><span style=\"font-family:Times New Roman;\">macs2 callpeak<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u4ea7\u751f<\/span><span style=\"font-family:Times New Roman;\">narrowPeak<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6587\u4ef6\uff0c\u9700\u8981\u9996\u5148\u5904\u7406\u4e00\u4e0b\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">awk ‘{print $4″t”$1″t”$2″t”$3″t+”}’ chirp_06ab_peaks.narrowPeak > chirp_06ab_homer.bed<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">for i in *_homer.bed;do j=${i%_homer.bed}; bsub -J macs2p -e %J.err -o %J.out -R span[hosts=1] -n 1 “findMotifsGenome.pl $i mm10 $j -len 8,10,12”;done<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.3 Analyzing custom FASTA files (findMotifs.pl, homer2)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">homers<span style=\"font-family:\u5b8b\u4f53;\">\u7684\u8bf4\u660e\u6587\u6863\uff1a<\/span><span style=\"font-family:Times New Roman;\">recommended that you have both target and background sequences, and in each case you should have several (preferably thousands) of sequences in each set that are roughly the same length<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5b8b\u4f53;\">\u9700\u8981\u76ee\u7684\u548c\u80cc\u666f\u57fa\u56e0\u7684\u5e8f\u5217\uff0c\u6240\u4ee5\u8fd9\u4e2a\u4e00\u822c\u7528\u7684\u6bd4\u8f83\u5c11\u4e00\u4e9b\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.4 Analyzing data for RNA motifs (findMotifs.pl\/findMotifsGenome.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">####<span style=\"font-family:\u5b8b\u4f53;\">\u548c\u5bfb\u627e<\/span><span style=\"font-family:Times New Roman;\">DNA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u533a\u522b\u5728\u4e8e\uff1a\u4f7f\u7528 <\/span><span style=\"font-family:Times New Roman;\">findMotifs.pl<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u548c <\/span><span style=\"font-family:Times New Roman;\">findMotifsGenome.pl<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u65f6\uff0c\u8981\u52a0\u4e0a <\/span><span style=\"font-family:Times New Roman;\">\u201c-rna\u201d<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u53c2\u6570\uff0c\u4ece\u800c\u53ea\u5bfb\u627e<\/span><span style=\"font-family:Times New Roman;\">RNA+<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u94fe\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\uff0c\u5e76\u4e14\u5339\u914d<\/span><span style=\"font-family:Times New Roman;\">\/<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u663e\u793a<\/span><span style=\"font-family:Times New Roman;\">U<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u800c\u4e0d\u662f<\/span><span style=\"font-family:Times New Roman;\">T<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">#######<span style=\"font-family:\u5b8b\u4f53;\">\u6ce8\u610f\uff01<\/span><span style=\"font-family:Times New Roman;\">HOMER<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5c1a\u672a\u5305\u542b<\/span><span style=\"font-family:Times New Roman;\">\u201cRNA motif\u201d<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5217\u8868\uff0c\u6240\u4ee5\u4e0d\u652f\u6301<\/span><span style=\"font-family:Times New Roman;\">\u201c<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5df2\u77e5<\/span><span style=\"font-family:Times New Roman;\">motif\u201d<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u7684\u5206\u6790\u3002\u5982\u679c\u4f7f\u7528<\/span><span style=\"font-family:Times New Roman;\">FASTA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6587\u4ef6\u683c\u5f0f\uff0c\u8bf7\u5728\u8f93\u5165\u6587\u4ef6\u4e2d\u4f7f\u7528<\/span><span style=\"font-family:Times New Roman;\">T<\/span><span style=\"font-family:\u5b8b\u4f53;\">\uff08<\/span><span style=\"font-family:Times New Roman;\">DNA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u7f16\u7801\uff09\u3002<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"># <span style=\"font-family:\u5b8b\u4f53;\">\u83b7\u53d6\u76ee\u6807\u5e8f\u5217\u5728\u4eba\u7c7b<\/span><span style=\"font-family:Times New Roman;\">mRNA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u4e0a\u805a\u96c6\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">findMotifs.pl genes.txt mouse MotifOutput\/ -rna -len 8<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"># <span style=\"font-family:\u5b8b\u4f53;\">\u5206\u6790<\/span><span style=\"font-family:Times New Roman;\">CLIP-Seq for RNA motifs<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">findMotifsGenome.pl fox2.clip.bed hg17 MotifOutput -rna<\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.5 Scanning for motif across the entire genome (scanMotifGenomeWide.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span 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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\",\"time\":\"2023-03-14 19:00:49\",\"timeStamp\":\"1678791649\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247485855&idx=1&sn=c56306e65753beb90e598c6c9b7d4666&chksm=cf7c995af80b104c0c3507312df9725467b82ee0e30e94c245c0ec1a78a6c3cd25c198420f6e#rd\" target=\"_blank\" rel=\"noopener\">\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span id=\"copyright_logo\" class=\"wx_tap_link js_wx_tap_highlight rich_media_meta icon_appmsg_tag appmsg_title_tag weui-wa-hotarea\">\u539f\u521b <\/span><span class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u679c <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-03-14 19:00:49<\/em><\/div>\n<p><content><\/p>\n<p style=\"white-space: normal;\" data-mpa-powered-by=\"yiban.io\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.18518518518518517\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_0CuCiczxXATRA1NT7QsFibQGILBxvQ-82.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAx2cF5xxW6pBGPmgTUt8qTlL9RiabvDGL72zZRhzS10IN01ZYt0CuCiczxXATRA1NT7QsFibQGILBxvQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"font-size: 16px;text-align: center;\" data-recalc-dims=\"1\" \/><\/p>\n<section style=\"white-space: normal;\">\n<section style=\"box-sizing: border-box;max-width: 100%;\">\n<section>\n<section style=\"box-sizing: border-box;max-width: 100%;\">\n<section>\n<section style=\"box-sizing: border-box;max-width: 100%;\">\n<section>\n<section style=\"box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"box-sizing: border-box;\">\n<section style=\"line-height: 1.8;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"box-sizing: border-box;\">\n<section style=\"box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;font-size: 16px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\">\n<section style=\"padding-right: 5px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;line-height: 0;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"transform: perspective(0px);transform-style: flat;box-sizing: border-box;\">\n<section style=\"text-align: center;transform: rotateY(180deg);line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 21px;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8823529\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/2_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/3_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/4_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_svg\/oYwP0cFmRU1GD1tysLsmLNIM78AS2IutDaNX2fF75dw9icJ9mn1Av9PtibYjXJzzhvZiaric9mJroULZzpxvu1CNECJiap0wuxqRI\/640?wx_fmt=svg'''\" data-type=\"svg\" data-w=\"170\" style=\"height: 18.4896px;vertical-align: middle;width: 20.9896px;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding: 3px 20px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;background-color: rgb(255, 128, 52);box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\">\n<p><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">Homer<span style=\"font-family:\u5b8b\u4f53;\">\u662f\u5e72\u561b\u7684\uff1f<\/span><\/span><\/strong><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"box-sizing: border-box;\">\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">HOMER<span style=\"font-family:\u5b8b\u4f53;\">\u662f\u4e00\u5957\u57fa\u4e8e <\/span><span style=\"font-family:Times New Roman;\">C++ <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u548c <\/span><span style=\"font-family:Times New Roman;\">Perl <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u8bed\u8a00\u7684\u7528\u4e8e <\/span><span style=\"font-family:Times New Roman;\">motif <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u67e5\u627e\u548c\u4e8c\u4ee3\u6570\u636e\u5206\u6790\u7684\u5de5\u5177\uff0c\u4e00\u822c\u9700\u8981\u4e24\u4e2a\u5e8f\u5217\u4f5c\u4e3a\u53c2\u6570\uff1a<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:Times New Roman;\">\u25cf <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u53c2\u8003\u5e8f\u5217\uff1a<\/span><span style=\"font-family:Times New Roman;\">hg19<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3001<\/span><span style=\"font-family:Times New Roman;\">mm10 <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u7b49\u57fa\u56e0\u7ec4\u5e8f\u5217\u3001<\/span><span style=\"font-family:Times New Roman;\">promoter <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217\u3001\u81ea\u5b9a\u4e49\u7684 <\/span><span style=\"font-family:Times New Roman;\">FASTA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:Times New Roman;\">\u25cf <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6240\u8981\u5206\u6790\u7684\u5e8f\u5217\uff1a<\/span><span style=\"font-family:Times New Roman;\">DNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6216 <\/span><span style=\"font-family:Times New Roman;\">RNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">HOMER <span style=\"font-family:\u5b8b\u4f53;\">\u9002\u7528\u4e8e\u5728\u5927\u89c4\u6a21\u6570\u636e\u4e2d\u5bfb\u627e <\/span><span style=\"font-family:Times New Roman;\">DNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6216 <\/span><span style=\"font-family:Times New Roman;\">RNA <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217\u7684 <\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002<\/span><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;font-size: 16px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\">\n<section style=\"padding-right: 5px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;line-height: 0;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"transform: perspective(0px);transform-style: flat;box-sizing: border-box;\">\n<section style=\"text-align: center;transform: rotateY(180deg);line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 21px;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8823529\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/2_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/3_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/4_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_svg\/oYwP0cFmRU1GD1tysLsmLNIM78AS2IutDaNX2fF75dw9icJ9mn1Av9PtibYjXJzzhvZiaric9mJroULZzpxvu1CNECJiap0wuxqRI\/640?wx_fmt=svg'''\" data-type=\"svg\" data-w=\"170\" style=\"height: 18.4896px;vertical-align: middle;width: 20.9896px;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding: 3px 20px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;background-color: rgb(255, 128, 52);box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\">\n<p><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"> <span style=\"font-family:\u5b8b\u4f53;\">\u90a3\u4ec0\u4e48\u662f <\/span><span style=\"font-family:Times New Roman;\">motif <\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5462\uff1f<\/span><\/span><\/strong><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"font-size: 16px;box-sizing: border-box;\">\n<p style=\"margin-right: 0pt;margin-left: 0pt;\"><br \/><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">motif<span style=\"font-family:\u5b8b\u4f53;\">\uff1a\u53cd\u590d\u51fa\u73b0\u7684\u6a21\u5f0f\uff0c\u5373\u4e00\u79cd\u7279\u5f81\u5e8f\u5217\uff0c\u6bd4\u5982 <\/span><span style=\"font-family:Times New Roman;\">sequence motif, structure motif, network motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002\u5b83\u6709\u6216\u8005\u53ef\u80fd\u6709\u4e00\u5b9a\u7684\u751f\u7269\u5b66\u529f\u80fd\u3002<\/span><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;font-size: 16px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\">\n<section style=\"padding-right: 5px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;line-height: 0;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"transform: perspective(0px);transform-style: flat;box-sizing: border-box;\">\n<section style=\"text-align: center;transform: rotateY(180deg);line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 21px;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8823529\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/2_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/3_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-03-14_\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790\/4_c9mJroULZzpxvu1CNECJiap0wuxqRI.svg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_svg\/oYwP0cFmRU1GD1tysLsmLNIM78AS2IutDaNX2fF75dw9icJ9mn1Av9PtibYjXJzzhvZiaric9mJroULZzpxvu1CNECJiap0wuxqRI\/640?wx_fmt=svg'''\" data-type=\"svg\" data-w=\"170\" style=\"height: 18.4896px;vertical-align: middle;width: 20.9896px;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding: 3px 20px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;max-width: 100%;height: auto;background-color: rgb(255, 128, 52);box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\">\n<p><strong><span style=\"font-size: 12pt;font-family: \u5b8b\u4f53;\">\u5177\u4f53\u5206\u6790\u6b65\u9aa4<\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.1 linux<span style=\"font-family: \u5b8b\u4f53;\">\u914d\u7f6e\u65b0\u73af\u5883<\/span><\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">conda create -n work puthon=3.8<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">conda activate work<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.2 homer<span style=\"font-family: \u5b8b\u4f53;\">\u5b89\u88c5<\/span><\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">conda install -c bioconda homer<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">##<span style=\"font-family:\u5b8b\u4f53;\">\u4e0b\u8f7d<\/span><span style=\"font-family:Times New Roman;\">configureHomer.pl<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">wget http:\/\/homer.ucsd.edu\/homer\/configureHomer.pl<\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">##<span style=\"font-family:\u5b8b\u4f53;\">\u4f7f\u7528<\/span><span style=\"font-family:Times New Roman;\">configureHomer.pl<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u914d\u7f6e<\/span><span style=\"font-family:Times New Roman;\">Homer<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">perl configureHomer.pl -install <o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">perl configureHomer.pl -install mm10<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3 homer<span style=\"font-family: \u5b8b\u4f53;\">\u5206\u6790<\/span><\/span><\/strong><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.1 Analyzing lists of genes with promoter motif analysis (findMotifs.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">############<span style=\"font-family:\u5b8b\u4f53;\">\u5bfb\u627e\u57fa\u56e0\u5217\u8868\u542f\u52a8\u5b50\u4e0a\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5bcc\u96c6<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">findMotifs.pl 3v3135F15Q001gene.txt mouse \/public\/home\/wjiang\/zhan\/work\/homer\/testdata -len 10<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.2 Analyzing genomic positions(findMotifsGenome.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">####<span style=\"font-family:\u5b8b\u4f53;\">\u8f93\u5165\u4e3a<\/span><span style=\"font-family:Times New Roman;\">bed<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6587\u4ef6\uff0c\u4e3b\u8981\u662f<\/span><span style=\"font-family:Times New Roman;\">chip-seq<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6570\u636e\u901a\u8fc7<\/span><span style=\"font-family:Times New Roman;\">macs2 callpeak<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u4ea7\u751f<\/span><span style=\"font-family:Times New Roman;\">narrowPeak<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6587\u4ef6\uff0c\u9700\u8981\u9996\u5148\u5904\u7406\u4e00\u4e0b\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">awk ‘{print $4″t”$1″t”$2″t”$3″t+”}’ chirp_06ab_peaks.narrowPeak > chirp_06ab_homer.bed<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">for i in *_homer.bed;do j=${i%_homer.bed}; bsub -J macs2p -e %J.err -o %J.out -R span[hosts=1] -n 1 “findMotifsGenome.pl $i mm10 $j -len 8,10,12”;done<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.3 Analyzing custom FASTA files (findMotifs.pl, homer2)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">homers<span style=\"font-family:\u5b8b\u4f53;\">\u7684\u8bf4\u660e\u6587\u6863\uff1a<\/span><span style=\"font-family:Times New Roman;\">recommended that you have both target and background sequences, and in each case you should have several (preferably thousands) of sequences in each set that are roughly the same length<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5b8b\u4f53;\">\u9700\u8981\u76ee\u7684\u548c\u80cc\u666f\u57fa\u56e0\u7684\u5e8f\u5217\uff0c\u6240\u4ee5\u8fd9\u4e2a\u4e00\u822c\u7528\u7684\u6bd4\u8f83\u5c11\u4e00\u4e9b\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.4 Analyzing data for RNA motifs (findMotifs.pl\/findMotifsGenome.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">####<span style=\"font-family:\u5b8b\u4f53;\">\u548c\u5bfb\u627e<\/span><span style=\"font-family:Times New Roman;\">DNA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5e8f\u5217\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u533a\u522b\u5728\u4e8e\uff1a\u4f7f\u7528 <\/span><span style=\"font-family:Times New Roman;\">findMotifs.pl<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u548c <\/span><span style=\"font-family:Times New Roman;\">findMotifsGenome.pl<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u65f6\uff0c\u8981\u52a0\u4e0a <\/span><span style=\"font-family:Times New Roman;\">\u201c-rna\u201d<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u53c2\u6570\uff0c\u4ece\u800c\u53ea\u5bfb\u627e<\/span><span style=\"font-family:Times New Roman;\">RNA+<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u94fe\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><span style=\"font-family:\u5b8b\u4f53;\">\uff0c\u5e76\u4e14\u5339\u914d<\/span><span style=\"font-family:Times New Roman;\">\/<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u663e\u793a<\/span><span style=\"font-family:Times New Roman;\">U<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u800c\u4e0d\u662f<\/span><span style=\"font-family:Times New Roman;\">T<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u3002<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">#######<span style=\"font-family:\u5b8b\u4f53;\">\u6ce8\u610f\uff01<\/span><span style=\"font-family:Times New Roman;\">HOMER<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5c1a\u672a\u5305\u542b<\/span><span style=\"font-family:Times New Roman;\">\u201cRNA motif\u201d<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5217\u8868\uff0c\u6240\u4ee5\u4e0d\u652f\u6301<\/span><span style=\"font-family:Times New Roman;\">\u201c<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u5df2\u77e5<\/span><span style=\"font-family:Times New Roman;\">motif\u201d<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u7684\u5206\u6790\u3002\u5982\u679c\u4f7f\u7528<\/span><span style=\"font-family:Times New Roman;\">FASTA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6587\u4ef6\u683c\u5f0f\uff0c\u8bf7\u5728\u8f93\u5165\u6587\u4ef6\u4e2d\u4f7f\u7528<\/span><span style=\"font-family:Times New Roman;\">T<\/span><span style=\"font-family:\u5b8b\u4f53;\">\uff08<\/span><span style=\"font-family:Times New Roman;\">DNA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u7f16\u7801\uff09\u3002<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"># <span style=\"font-family:\u5b8b\u4f53;\">\u83b7\u53d6\u76ee\u6807\u5e8f\u5217\u5728\u4eba\u7c7b<\/span><span style=\"font-family:Times New Roman;\">mRNA<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u4e0a\u805a\u96c6\u7684<\/span><span style=\"font-family:Times New Roman;\">motif<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">findMotifs.pl genes.txt mouse MotifOutput\/ -rna -len 8<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"># <span style=\"font-family:\u5b8b\u4f53;\">\u5206\u6790<\/span><span style=\"font-family:Times New Roman;\">CLIP-Seq for RNA motifs<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">findMotifsGenome.pl fox2.clip.bed hg17 MotifOutput -rna<\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(255, 169, 0);\"><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\">3.3.5 Scanning for motif across the entire genome (scanMotifGenomeWide.pl)<\/span><\/strong><\/span><strong><span style=\"font-family: "Times New Roman";font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">scanMotifGenomeWide.pl pu1.motif mm9 -bed > pu1.sites.mm9.bed<o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\">########<span style=\"font-family:\u5b8b\u4f53;\">\u8fd9\u4e2a\u7684\u8bdd\uff0c<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:'Times New Roman';mso-hansi-font-family:'Times New Roman';mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u5176\u5b9e<\/span><span style=\"mso-spacerun:'yes';font-family:'Times New Roman';mso-fareast-font-family:\u5b8b\u4f53;font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5b8b\u4f53;\">\u7528<\/span>MEME<span style=\"font-family:\u5b8b\u4f53;\">\u6570\u636e\u5e93\u4e2d\u7684<\/span><span style=\"font-family:Times New Roman;\">FIMO<\/span><span style=\"font-family:\u5b8b\u4f53;\">\u6548\u679c\u66f4\u597d\u4e00\u4e9b<\/span><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"font-size: 16px;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\" style=\"line-height: 28.8px;max-width: none;overflow-wrap: break-word;box-sizing: border-box;min-height: 0px;background-image: none;background-clip: border-box;background-position: 0% 0%;background-repeat: repeat;background-size: auto;border-width: 0px;border-style: none;border-color: rgb(51, 51, 51);bottom: auto;float: none;height: 55.5556px;left: auto;max-height: none;min-width: 0px;text-decoration-style: solid;text-decoration-color: rgb(51, 51, 51);top: auto;z-index: auto;visibility: visible;clear: none;\">\n<p style=\"text-indent: 0em;box-sizing: border-box;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 20px;font-size: 16px;display: flex;flex-flow: row nowrap;text-align: center;justify-content: center;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 543.108px;vertical-align: top;border-style: solid;border-width: 1px;border-color: rgb(67, 67, 67);flex: 0 0 auto;align-self: flex-start;height: auto;box-shadow: rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 378.611px;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;box-sizing: border-box;\">\n<section style=\"text-align: center;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\"><span style=\"font-size: 15px;box-sizing: border-box;\">\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/p>\n<p style=\"box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\"><span style=\"font-size: 15px;box-sizing: border-box;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/p>\n<p style=\"box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\"><span style=\"font-size: 15px;box-sizing: border-box;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/p>\n<p style=\"box-sizing: border-box;\"><span style=\"color: rgb(255, 129, 36);box-sizing: border-box;font-size: 12px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;width: 162.257px;vertical-align: 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