{"id":71563,"date":"2026-11-15T01:21:29","date_gmt":"2026-11-14T17:21:29","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71563"},"modified":"2026-11-15T01:21:29","modified_gmt":"2026-11-14T17:21:29","slug":"miniprot-protein-coverage-frameshift-one-base-exon","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/miniprot-protein-coverage-frameshift-one-base-exon\/","title":{"rendered":"miniprot \u5b9e\u8dd1\uff5c\u86cb\u767d\u4ece\u7b2c 1 \u5230\u7b2c 300 \u4f4d\u90fd\u6bd4\u4e0a\u4e86\uff0c\u4e3a\u4ec0\u4e48\u57fa\u56e0\u6a21\u578b\u91cc\u4ecd\u6709\u4e00\u6b21\u79fb\u7801\uff1f"},"content":{"rendered":"
\n

\u5728\u65b0\u7ec4\u88c5\u4e0a\u5bfb\u627e\u5df2\u77e5\u86cb\u767d\u65f6\uff0c\u6700\u5148\u770b\u7684\u901a\u5e38\u662f\u8986\u76d6\u7387\u548c\u4e00\u81f4\u6027\u3002\u4e00\u6761\u4e09\u767e\u6c28\u57fa\u9178\u7684\u86cb\u767d\u4ece\u5934\u6bd4\u5230\u5c3e\u3001\u4e00\u81f4\u6027\u8d85\u8fc7\u767e\u5206\u4e4b\u4e5d\u5341\u4e5d\uff0c\u662f\u5426\u53ef\u4ee5\u76f4\u63a5\u636e\u6b64\u8ba4\u5b9a\u7f16\u7801\u5e8f\u5217\u5b8c\u6574\uff1f\u6211\u4eec\u5b89\u88c5 miniprot\uff0c\u4eba\u5de5\u9020\u51fa\u542b\u4e00\u4e2a\u5185\u542b\u5b50\u7684\u5b8c\u6574\u57fa\u56e0\uff0c\u518d\u4ece\u7f16\u7801\u533a\u53bb\u6389\u4e00\u4e2a\u6838\u82f7\u9178\u3002\u4e24\u6761\u7ed3\u679c\u90fd\u8986\u76d6\u540c\u4e00\u86cb\u767d\u7684\u5168\u90e8\u4e09\u767e\u4e2a\u6c28\u57fa\u9178\uff0c\u53ea\u6709\u7b2c\u4e8c\u6761\u5728\u57fa\u56e0\u6a21\u578b\u4e2d\u62a5\u544a\u79fb\u7801\u3002\u8fd9\u4e2a\u5bf9\u7167\u53ef\u4ee5\u5e2e\u52a9\u533a\u5206\u4e09\u4e2a\u4e0d\u540c\u7684\u95ee\u9898\uff0c\u86cb\u767d\u6709\u6ca1\u6709\u627e\u5230\u3001\u526a\u63a5\u4f4d\u7f6e\u662f\u5426\u5408\u7406\u3001\u9605\u8bfb\u6846\u662f\u5426\u8fde\u7eed\u3002miniprot \u5b98\u65b9\u9879\u76ee<\/a><\/p>\n

\u4e3a\u4ec0\u4e48\u86cb\u767d\u6bd4\u5bf9\u4f1a\u5bb9\u8bb8\u79fb\u7801<\/h2>\n

\u628a\u4e00\u6761\u57fa\u56e0\u7ec4 DNA \u76f4\u63a5\u7ffb\u8bd1\uff0c\u4e09\u4e2a\u6838\u82f7\u9178\u5bf9\u5e94\u4e00\u4e2a\u6c28\u57fa\u9178\u3002\u82e5\u5728\u5916\u663e\u5b50\u4e2d\u95f4\u5c11\u4e86\u4e00\u4e2a\u78b1\u57fa\uff0c\u4ece\u8fd9\u4e00\u5904\u7ee7\u7eed\u6bcf\u4e09\u4f4d\u5f80\u540e\u8bfb\uff0c\u540e\u9762\u7684\u5bc6\u7801\u5b50\u7ec4\u5408\u901a\u5e38\u90fd\u4f1a\u6539\u53d8\u3002\u4e00\u4e2a\u8003\u8651\u79fb\u7801\u7684\u86cb\u767d\u5230\u57fa\u56e0\u7ec4\u6bd4\u5bf9\u5668\uff0c\u53ef\u4ee5\u5728\u5c40\u90e8\u4f4d\u7f6e\u4ed8\u51fa\u60e9\u7f5a\uff0c\u6cbf\u53e6\u4e00\u9605\u8bfb\u6846\u7ee7\u7eed\u5bfb\u627e\u4e0b\u6e38\u540c\u6e90\u7247\u6bb5\u3002\u8fd9\u6837\u505a\u6709\u52a9\u4e8e\u5728\u7ec4\u88c5\u9519\u8bef\u3001\u7591\u4f3c\u5047\u57fa\u56e0\u6216\u4e0d\u5b8c\u6574\u9884\u6d4b\u4e2d\u8bc6\u522b\u540c\u6e90\u86cb\u767d\u3002\u4e5f\u6b63\u56e0\u4e3a\u5b83\u80fd\u8de8\u8fc7\u969c\u788d\uff0c\u5b8c\u6574\u7684\u86cb\u767d\u67e5\u8be2\u8986\u76d6\u7387\u4e0d\u80fd\u5355\u72ec\u4f5c\u4e3a\u5f00\u653e\u9605\u8bfb\u6846\u5b8c\u6574\u7684\u8bc1\u636e\u3002\u4f5c\u8005\u53d1\u5e03\u7684 miniprot \u624b\u518c<\/a><\/p>\n

\u8fd8\u8981\u5206\u6e05\u5185\u542b\u5b50\u548c\u5916\u663e\u5b50\u5185\u90e8\u7684\u5f02\u5e38\u3002\u8de8\u8d8a\u957f\u5185\u542b\u5b50\u65f6\uff0c\u57fa\u56e0\u7ec4\u5750\u6807\u4f1a\u5411\u524d\u8df3\u5f88\u591a\uff0c\u86cb\u767d\u67e5\u8be2\u4ecd\u53ef\u4ee5\u8fde\u7eed\u3002\u5bf9\u4e8e\u6b63\u5e38\u7684\u526a\u63a5\uff0c\u6b63\u786e\u62fc\u63a5\u540e\u7684\u8f6c\u5f55\u672c\u53ef\u4ee5\u7ef4\u6301\u9605\u8bfb\u6846\u3002\u5916\u663e\u5b50\u5185\u90e8\u5c11\u4e00\u4e2a\u6838\u82f7\u9178\uff0c\u5219\u53d1\u751f\u5728\u5e94\u88ab\u7ffb\u8bd1\u7684\u5e8f\u5217\u91cc\uff0c\u8981\u68c0\u67e5\u8bfb\u6bb5\u3001\u7ec4\u88c5\u548c\u8f6c\u5f55\u672c\u80fd\u5426\u89e3\u91ca\u3002\u4e24\u79cd\u4fe1\u53f7\u90fd\u53ef\u4ee5\u51fa\u73b0\u5728\u4e00\u4efd\u957f\u8ddd\u79bb\u6bd4\u5bf9\u4e2d\uff0c\u53ea\u770b\u57fa\u56e0\u7ec4\u8d77\u6b62\u5750\u6807\u548c\u8986\u76d6\u7387\u5f88\u96be\u628a\u5b83\u4eec\u5206\u5f00\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4fdd\u7559 1800 bp \u5185\u542b\u5b50\uff0c\u53ea\u5220\u9664\u4e00\u4e2a\u7f16\u7801\u78b1\u57fa<\/h2>\n

\u6211\u4eec\u7528\u56fa\u5b9a\u79cd\u5b50\u751f\u6210\u4e09\u767e\u6c28\u57fa\u9178\u7684\u4eba\u5de5\u86cb\u767d\uff0c\u4e3a\u6bcf\u4e2a\u6c28\u57fa\u9178\u6307\u5b9a\u4e00\u4e2a\u6807\u51c6\u9057\u4f20\u5bc6\u7801\u8868\u4e2d\u7684\u5bc6\u7801\u5b50\uff0c\u5f97\u5230\u4e5d\u767e\u78b1\u57fa\u7f16\u7801\u533a\u3002\u5c06\u7f16\u7801\u533a\u4ece\u4e2d\u95f4\u5206\u6210\u4e24\u6bb5\uff0c\u63d2\u5165\u4e00\u5343\u516b\u767e\u4e2a\u78b1\u57fa\u7684\u4eba\u5de5\u5185\u542b\u5b50\uff0c\u4fdd\u7559\u5e38\u89c1\u7684 GT \u4f9b\u4f53\u548c AG \u53d7\u4f53\uff0c\u5728\u672b\u7aef\u53e6\u5916\u653e\u7f6e\u7ec8\u6b62\u5bc6\u7801\u5b50\u3002\u5bf9\u7167\u7ec4\u53ea\u4ece\u7b2c\u4e8c\u4e2a\u5916\u663e\u5b50\u5220\u53bb\u539f\u7f16\u7801\u533a\u4e00\u5f00\u59cb\u8ba1\u6570\u7684\u7b2c\u516d\u767e\u96f6\u4e00\u4e2a\u78b1\u57fa\u3002\u4e24\u6b21\u90fd\u7528\u540c\u4e00\u6761\u86cb\u767d\u3001\u540c\u4e00\u7248\u672c 0.18-r281 \u548c\u76f8\u540c\u53c2\u6570\u5b9e\u9645\u6bd4\u5bf9\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u68c0\u67e5\u6307\u6807<\/th>\n\u5b8c\u6574\u57fa\u56e0<\/th>\n\u7f3a\u4e00\u4e2a\u7f16\u7801\u78b1\u57fa<\/th>\n<\/tr>\n<\/thead>\n
\u67e5\u8be2\u8986\u76d6<\/td>\n1\u2013300\uff0c\u5168\u90e8<\/td>\n1\u2013300\uff0c\u5168\u90e8<\/td>\n<\/tr>\n
\u4e24\u4e2a CDS \u5bf9\u5e94\u7684\u86cb\u767d\u533a\u95f4<\/td>\n1\u2013150\u3001151\u2013300<\/td>\n1\u2013150\u3001151\u2013300<\/td>\n<\/tr>\n
mRNA \u4e00\u81f4\u6027\u4e0e\u79fb\u7801<\/td>\n1.0000\uff0c\u79fb\u7801\u8ba1\u6570 0<\/td>\n0.9967\uff0c\u79fb\u7801\u8ba1\u6570 1<\/td>\n<\/tr>\n
\u6bd4\u5bf9\u64cd\u4f5c\u4e32<\/td>\n150M1800N150M<\/td>\n150M1800N49M2G100M<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u4e24\u7248\u90fd\u627e\u5230\u4e86\u957f\u5ea6\u76f8\u540c\u7684\u5185\u542b\u5b50\uff0c\u9996\u4e2a\u7f16\u7801\u533a\u7684\u57fa\u56e0\u7ec4\u5750\u6807\u4e5f\u4e00\u6837\uff0c\u4ece\u7b2c\u4e00\u5343\u4e8c\u767e\u96f6\u4e00\u5230\u7b2c\u4e00\u5343\u516d\u767e\u4e94\u5341\u4f4d\u3002\u5220\u78b1\u57fa\u540e\uff0c\u7b2c\u4e8c\u4e2a\u7f16\u7801\u533a\u4ecd\u4ece\u7b2c\u4e09\u5343\u56db\u767e\u4e94\u5341\u4e00\u4f4d\u5f00\u59cb\uff0c\u672b\u7aef\u6bd4\u5b8c\u6574\u7ec4\u63d0\u524d\u4e00\u4e2a\u78b1\u57fa\u3002\u7f3a\u5931\u7ec4\u7684\u8be6\u7ec6 GFF \u4e2d\uff0c\u7b2c\u4e00\u6bb5 CDS \u7684\u4e00\u81f4\u6027\u4ecd\u4e3a\u4e00\uff0c\u7b2c\u4e8c\u6bb5\u53d8\u4e3a\u96f6\u70b9\u4e5d\u4e5d\u4e09\u4e09\uff0c\u5e76\u5355\u72ec\u5e26\u4e0a\u4e00\u6b21\u79fb\u7801\u6807\u8bb0\u3002\u6a21\u578b\u603b\u5206\u4ece\u4e00\u5343\u516d\u767e\u4e5d\u5341\u516d\u51cf\u5230\u4e00\u5343\u516d\u767e\u516d\u5341\u4e5d\u3002\u5c06\u5168\u6a21\u578b\u548c\u5404\u5916\u663e\u5b50\u7684\u6307\u6807\u653e\u5728\u4e00\u8d77\uff0c\u624d\u53ef\u4ee5\u76f4\u63a5\u5b9a\u4f4d\u5e94\u56de\u67e5\u54ea\u4e00\u6bb5\u5e8f\u5217\u3002<\/p>\n

\"\u8986\u76d6
\u4fdd\u7559 1800 bp \u5185\u542b\u5b50\uff0c\u5728\u7b2c\u4e8c\u4e2a\u5916\u663e\u5b50\u4e2d\u5220\u9664\u4e00\u4e2a\u78b1\u57fa\u3002<\/figcaption><\/figure>\n

\u8c01\u7684\u5750\u6807\uff0c\u8c01\u7684\u957f\u5ea6<\/h2>\n

miniprot \u7684 PAF \u6837\u5f0f\u8f93\u51fa\u6709\u86cb\u767d\u67e5\u8be2\u4e0e\u57fa\u56e0\u7ec4\u76ee\u6807\u4e24\u79cd\u5355\u4f4d\u3002\u793a\u4f8b\u4e2d\u76ee\u6807\u662f DNA\uff0c\u67e5\u8be2\u662f\u6c28\u57fa\u9178\uff0c\u64cd\u4f5c\u4e32\u8fd8\u4f1a\u8868\u8fbe\u526a\u63a5\u4e0e\u79fb\u7801\u3002\u4e0d\u80fd\u628a\u5176\u4e2d\u6bcf\u4e2a\u6570\u5b57\u90fd\u7167\u77ed\u8bfb\u6bb5\u6838\u82f7\u9178\u6bd4\u5bf9\u7684\u4e60\u60ef\u89e3\u91ca\u3002\u8fd9\u91cc\u7684 1800N<\/code> \u4e0e\u5efa\u6a21\u65f6\u63d2\u5165\u7684\u5185\u542b\u5b50\u957f\u5ea6\u4e00\u81f4\uff0c\u5de6\u53f3\u7684 150M<\/code> \u5728\u5b8c\u6574\u5bf9\u7167\u4e2d\u5206\u522b\u5bf9\u5e94\u4e00\u767e\u4e94\u5341\u4e2a\u6c28\u57fa\u9178\u3002\u7f3a\u5931\u5bf9\u7167\u91cc\u7684 2G<\/code> \u662f\u8fd9\u7248\u86cb\u767d\u6bd4\u5bf9\u5bf9\u5c40\u90e8\u5f02\u5e38\u7684\u7279\u5b9a\u7f16\u7801\uff0c\u4e0d\u5e94\u8bfb\u6210 DNA \u91cc\u53c8\u51fa\u73b0\u4e86\u4e24\u4e2a\u65b0\u589e\u7a81\u53d8\u3002\u53ef\u4fe1\u7684\u5df2\u77e5\u53d8\u5316\u53ea\u6709\u811a\u672c\u5220\u6389\u7684\u4e00\u4e2a\u78b1\u57fa\u3002miniprot \u5bf9\u86cb\u767d\u6bd4\u5bf9\u548c\u79fb\u7801\u64cd\u4f5c\u7684\u5b9a\u4e49<\/a><\/p>\n

miniprot --gff --aln -t 1 intact.fa protein.fa > intact.gff\r\nminiprot --gff --aln -t 1 deletion.fa protein.fa > deletion.gff\r\nawk -F '\\t' '!\/^#\/ && ($3=="mRNA" || $3=="CDS")' deletion.gff\r\n<\/code><\/pre>\n
\u5982\u679c\u4ece GFF \u63d0\u53d6\u57fa\u56e0\u7ec4\u5e8f\u5217\u505a\u9a8c\u8bc1\uff0c\u8fd8\u8981\u6838\u5bf9\u672b\u7aef\u7ec8\u6b62\u5bc6\u7801\u5b50\u7684\u5904\u7406\u3002\u8fd9\u6b21\u5b8c\u6574\u7ec4\u7684\u7b2c\u4e8c\u6bb5 CDS \u5750\u6807\u5230\u7b2c\u4e09\u5343\u4e5d\u767e\u96f6\u4e09\u4f4d\uff0c\u6700\u540e\u4e09\u4f4d\u53c8\u5355\u72ec\u5728 stop_codon<\/code> \u884c\u7ed9\u51fa\u3002\u4e24\u6761\u8bb0\u5f55\u7684\u78b1\u57fa\u5728\u5750\u6807\u4e0a\u91cd\u53e0\u3002\u82e5\u628a\u7ec8\u6b62\u5bc6\u7801\u5b50\u5f53\u4f5c\u989d\u5916\u4e00\u6bb5\u518d\u62fc\u4e00\u6b21\uff0c\u4f1a\u5728\u672b\u5c3e\u4eba\u4e3a\u591a\u51fa\u4e09\u4e2a\u78b1\u57fa\u3002\u7528\u53c2\u8003 FASTA \u6309\u5750\u6807\u548c\u94fe\u65b9\u5411\u63d0\u53d6\uff0c\u5148\u68c0\u67e5\u5404\u6bb5\u62fc\u63a5\u540e\u7684\u603b\u957f\uff0c\u518d\u7ffb\u8bd1\u5e76\u5bf9\u9f50\u539f\u86cb\u767d\uff0c\u80fd\u53ca\u65e9\u53d1\u73b0\u91cd\u590d\u62fc\u63a5\u3001\u5750\u6807\u8d77\u70b9\u504f\u79fb\u548c\u65b9\u5411\u5904\u7406\u9519\u8bef\u3002<\/p>\n
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