{"id":34605,"date":"2024-12-09T21:56:27","date_gmt":"2024-12-09T13:56:27","guid":{"rendered":"https:\/\/17aitech.com\/?p=34605"},"modified":"2024-12-09T21:56:27","modified_gmt":"2024-12-09T13:56:27","slug":"%e5%9f%ba%e4%ba%8etransformer%e7%9a%84%e6%96%b0%e6%96%b9%e6%b3%95%ef%bc%8c%e5%8f%af%e4%bb%8e%e7%ba%b3%e7%b1%b3%e5%ad%94%e6%b5%8b%e5%ba%8f%e4%b8%ad%e5%87%86%e7%a1%ae%e9%a2%84%e6%b5%8bdna%e7%94%b2","status":"publish","type":"post","link":"https:\/\/17aitech.com\/?p=34605","title":{"rendered":"\u57fa\u4e8eTransformer\u7684\u65b0\u65b9\u6cd5\uff0c\u53ef\u4ece\u7eb3\u7c73\u5b54\u6d4b\u5e8f\u4e2d\u51c6\u786e\u9884\u6d4bDNA\u7532\u57fa\u5316"},"content":{"rendered":"

\u6587\u7ae0\u6765\u6e90\u4e8e\u4e92\u8054\u7f51:\u57fa\u4e8eTransformer\u7684\u65b0\u65b9\u6cd5\uff0c\u53ef\u4ece\u7eb3\u7c73\u5b54\u6d4b\u5e8f\u4e2d\u51c6\u786e\u9884\u6d4bDNA\u7532\u57fa\u5316<\/a><\/p>\n

<\/a><\/p>\n

\u7f16\u8f91 | \u841d\u535c\u76ae<\/p>\n

DNA \u7532\u57fa\u5316\u5728\u5404\u79cd\u751f\u7269\u8fc7\u7a0b\u4e2d\u8d77\u7740\u91cd\u8981\u4f5c\u7528\uff0c\u5305\u62ec\u7ec6\u80de\u5206\u5316\u3001\u8870\u8001\u548c\u764c\u75c7\u53d1\u5c55\u3002\u54fa\u4e73\u52a8\u7269\u4e2d\u6700\u91cd\u8981\u7684\u7532\u57fa\u5316\u662f5-\u7532\u57fa\u80de\u5627\u5576\uff0c\u4e3b\u8981\u53d1\u751f\u5728 CpG \u4e8c\u6838\u82f7\u9178\u7684\u80cc\u666f\u4e0b\u3002<\/p>\n

\u5168\u57fa\u56e0\u7ec4\u4e9a\u786b\u9178\u76d0\u6d4b\u5e8f\u7b49\u6d4b\u5e8f\u65b9\u6cd5\u53ef\u4ee5\u6210\u529f\u68c0\u6d4b 5-\u7532\u57fa\u80de\u5627\u5576 DNA \u4fee\u9970\u3002\u7136\u800c\uff0c\u5b83\u4eec\u5b58\u5728\u8bfb\u53d6\u957f\u5ea6\u77ed\u7684\u4e25\u91cd\u7f3a\u9677\uff0c\u53ef\u80fd\u4f1a\u5f15\u5165\u6269\u589e\u504f\u5dee\u3002<\/p>\n

\u65b0\u52a0\u5761\u00a0A*STAR \u7684\u7814\u7a76\u4eba\u5458\u5f00\u53d1\u4e86\u4e00\u79cd\u6df1\u5ea6\u5b66\u4e60<\/mark>\u7b97\u6cd5 Rockfish\uff0c\u8be5\u7b97\u6cd5\u901a\u8fc7\u4f7f\u7528\u7eb3\u7c73\u5b54\u6d4b\u5e8f\uff08Oxford Nanopore Sequencing\uff0cONT\uff09\u663e\u8457\u63d0\u9ad8\u4e86\u8bfb\u53d6\u7ea7 5-\u7532\u57fa\u80de\u5627\u5576\u68c0\u6d4b\u80fd\u529b\u3002<\/p>\n

\u8be5\u7814\u7a76\u4ee5\u300cRockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing<\/em>\u300d\u4e3a\u9898\uff0c\u4e8e 2024 \u5e74 7 \u6708 3 \u65e5\u53d1\u5e03\u5728\u300aNature Communications<\/em>\u300b\u3002<\/p>\n

<\/a><\/p>\n

\u8003\u8651\u5230\u9700\u8981\u4e00\u79cd\u9ad8\u7cbe\u5ea6\u7684\u8bfb\u53d6\u7ea7\u522b\u9884\u6d4b\u65b9\u6cd5\uff0c\u7814\u7a76\u4eba\u5458\u7740\u624b\u4f7f\u7528\u73b0\u4ee3\u67b6\u6784 Transformers \u5f00\u53d1\u4e00\u79cd\u65b0\u7684\u3001\u6700\u5148\u8fdb\u7684\u6df1\u5ea6\u5b66\u4e60<\/mark>\u65b9\u6cd5\u3002\u4ed6\u4eec\u7684\u65b9\u6cd5 Rockfish \u4f9d\u8d56\u4e8e\u539f\u59cb\u7eb3\u7c73\u5b54\u4fe1\u53f7\u3001\u6838\u78b1\u57fa\u5e8f\u5217\u548c\u6bd4\u5bf9\u4fe1\u606f\u6765\u68c0\u6d4b 5mC \u4fee\u9970\u3002<\/p>\n

<\/a><\/p>\n

\u56fe\u793a\uff1aRockfish \u67b6\u6784\u6982\u8ff0\u3002\uff08\u6765\u6e90\uff1a\u8bba\u6587\uff09<\/section>\n

\u7814\u7a76\u4eba\u5458\u4f7f\u7528\u9ad8\u8d28\u91cf\u7684\u4eba\u7c7b\u548c\u5c0f\u9f20\u6570\u636e\u96c6\u8bad\u7ec3\u8be5\u6a21\u578b\uff0c\u5e76\u5728\u591a\u4e2a R9.4.1 \u548c R10.4.1 \u6570\u636e\u96c6\u4e0a\u5bf9\u5176\u8fdb\u884c\u6d4b\u8bd5\uff0c\u5305\u62ec\u5185\u90e8\u6d4b\u5e8f\u7684 R9.4.1 H1 \u80da\u80ce\u5e72\u7ec6\u80de (H1ESc) \u539f\u751f\u6570\u636e\u96c6\u548c R9.4.1 \u548c R10.4.1 \u65b0\u751f\u5c0f\u9f20 (C57BL\/6 \u65b0\u751f\u513f) \u6570\u636e\uff0c\u4ee5\u53ca\u4e00\u4e9b\u516c\u5f00\u53ef\u7528\u7684\u4eba\u7c7b\u764c\u75c7\u548c\u8840\u6db2\u6570\u636e\u96c6\u3002<\/p>\n

\u9274\u4e8e R9.4.1 \u548c R10.4.1 NA12878 \u4ee5\u53ca\u65b0\u751f\u5c0f\u9f20\u6570\u636e\u96c6\u5747\u7528\u4e8e\u8bc4\u4f30\uff0c\u7814\u7a76\u4eba\u5458\u6307\u51fa\u4e86\u5b54\u7248\u672c\u4ee5\u533a\u5206\u5b83\u4eec\u3002\u5176\u4f59\u6570\u636e\u96c6\u4ec5\u4f7f\u7528 R9.4.1 \u5b54\u7248\u672c\u8fdb\u884c\u6d4b\u5e8f\u3002<\/p>\n

\u5bf9 Rockfish \u6a21\u578b\u8fdb\u884c\u4e86\u5e7f\u6cdb\u7684\u8bc4\u4f30\uff0c\u5e76\u4e0e R9.4.1 \u6570\u636e\u96c6\u7684 Megalodon Remora\u3001Megalodon Rerio \u548c Nanopolish \u4ee5\u53ca R10.4.1 \u6570\u636e\u96c6\u7684 Remora \u8fdb\u884c\u4e86\u6bd4\u8f83\uff0c\u6bd4\u8f83\u5185\u5bb9\u5305\u62ec\u4ee5\u4e0b\u516d\u4e2a\u65b9\u9762\uff1a\u8bfb\u6bb5\u7ea7\u9884\u6d4b\u3001\u4f4d\u70b9\u7ea7\u9884\u6d4b\u3001\u4e0e WGBS \u7684\u4f4d\u70b9\u7ea7\u76f8\u5173\u6027\u3001\u8c03\u7528\u8986\u76d6\u5ea6\u3001\u6267\u884c\u65f6\u95f4\u548c\u8d44\u6e90\u5229\u7528\u7387\u3002<\/p>\n

<\/a><\/p>\n

\u56fe\u793a\uff1aRead-level \u8bc4\u4f30\u3002\uff08\u6765\u6e90\uff1a\u8bba\u6587\uff09<\/p>\n

\u5728 R.9.4.1 \u6570\u636e\u96c6\u4e0a\u5355\u78b1\u57fa\u51c6<\/mark>\u786e\u7387\u548c F1 \u5ea6\u91cf\u503c\u63d0\u9ad8\u4e86\u6700\u591a 5 \u4e2a\u767e\u5206\u70b9\uff0c\u5728 R10.4.1 \u6570\u636e\u96c6\u4e0a\u63d0\u9ad8\u4e86\u6700\u591a 0.82 \u4e2a\u767e\u5206\u70b9\u3002<\/p>\n

\u6b64\u5916\uff0cRockfish \u4e0e\u5168\u57fa\u56e0\u7ec4\u4e9a\u786b\u9178\u76d0\u6d4b\u5e8f\u8868\u73b0\u51fa\u9ad8\u5ea6\u76f8\u5173\u6027\uff0c\u9700\u8981\u7684\u8bfb\u53d6\u6df1\u5ea6\u8f83\u4f4e\uff0c\u5e76\u4e14\u5728\u8ba1\u7b97\u6548\u7387\u9ad8\u7684\u540c\u65f6\u5bf9\u5bcc\u542b CpG \u7684\u542f\u52a8\u5b50\u7b49\u751f\u7269\u5b66\u91cd\u8981\u533a\u57df\u5177\u6709\u66f4\u9ad8\u7684\u7f6e\u4fe1\u5ea6\u3002<\/p>\n

\u5b83\u5728\u4eba\u7c7b\u548c\u5c0f\u9f20\u6837\u672c\u4e2d\u7684\u4f18\u5f02\u8868\u73b0\u51f8\u663e\u4e86\u5176\u5728\u7814\u7a76\u4e0d\u540c\u751f\u7269\u4f53\u548c\u75be\u75c5\u4e2d\u7684 5-\u7532\u57fa\u80de\u5627\u5576\u7532\u57fa\u5316\u65b9\u9762\u7684\u591a\u529f\u80fd\u6027\u3002\u6700\u540e\uff0c\u5176\u9002\u5e94\u6027\u67b6\u6784\u786e\u4fdd\u4e0e\u65b0\u7248\u672c\u7684\u5b54\u548c\u5316\u5b66\u4ee5\u53ca\u4fee\u9970\u7c7b\u578b\u517c\u5bb9\u3002<\/p>\n

<\/a><\/p>\n

\u56fe\u793a\uff1a\u57fa\u4e8e ONT \u7684\u5de5\u5177\u4e0e WGBS \u4e4b\u95f4\u7684\u76f8\u5173\u6027\u5206\u6790\u3002\uff08\u6765\u6e90\uff1a\u8bba\u6587\uff09<\/section>\n

\u4e0d\u8fc7\uff0cRockfish \u76ee\u524d\u65e0\u6cd5\u533a\u5206 5mC \u548c 5hmC \u7532\u57fa\u5316\uff0c\u56e0\u4e3a\u7f3a\u4e4f\u9ad8\u8d28\u91cf\u7684\u5176\u4ed6\u7c7b\u578b\u4fee\u9970\u7684\u5bf9\u7167\u6570\u636e\u96c6\u3002\u6a21\u578b\u5728\u8ba1\u7b97\u6548\u7387\u4e0a\u4ecd\u6709\u6539\u8fdb\u7a7a\u95f4\uff0c\u672a\u6765\u53ef\u80fd\u901a\u8fc7\u67b6\u6784\u548c\u5de5\u7a0b\u4f18\u5316\u63d0\u9ad8\u6548\u7387\u3002<\/p>\n

Rockfish \u5c55\u793a\u4e86\u4ece ONT \u539f\u59cb\u4fe1\u53f7\u4e2d\u63d0\u53d6\u7532\u57fa\u5316\u4fe1\u606f\u7684\u5f3a\u5927\u80fd\u529b\uff0c\u5176\u5c0f\u578b\u6a21\u578b\u5728\u6240\u6709\u6570\u636e\u96c6\u4e0a\u6027\u80fd\u66f4\u4f18\uff0c\u8fd0\u884c\u65f6\u95f4\u66f4\u77ed\uff0c\u5c55\u73b0\u4e86\u989d\u5916\u6570\u636e\u548c\u77e5\u8bc6\u84b8\u998f<\/mark>\u7684\u597d\u5904\u3002<\/p>\n

5mC \u4fee\u9970\u4e0e\u591a\u79cd\u751f\u7269\u5b66\u73b0\u8c61\u76f8\u5173\uff0c\u5982\u8f6c\u5f55\u8c03\u63a7\u3001\u75be\u75c5\u3001\u8870\u8001\u7b49\uff0c\u56e0\u6b64\u5355\u78b1\u57fa\u5206\u8fa8\u7387\u7684\u68c0\u6d4b\u5bf9\u4e8e\u6df1\u5165\u7406\u89e3 DNA \u7532\u57fa\u5316\u7684\u4f5c\u7528\u81f3\u5173\u91cd\u8981\uff0c\u53ef\u80fd\u6709\u52a9\u4e8e\u75be\u75c5\u7684\u65e9\u671f\u8bca\u65ad\u548c\u6cbb\u7597\u7b56\u7565\u9009\u62e9\u3002Rockfish \u7684\u67b6\u6784\u4f7f\u5176\u6613\u4e8e\u6269\u5c55\u5230\u68c0\u6d4b\u5404\u79cd\u7c7b\u578b\u7684 DNA \u548c RNA \u4fee\u9970\u3002<\/p>\n

\u8bba\u6587\u94fe\u63a5\uff1ahttps:\/\/www.nature.com\/articles\/s41467-024-49847-0<\/em><\/p>\n

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