{"id":72698,"date":"2026-11-15T09:54:13","date_gmt":"2026-11-15T01:54:13","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=72698"},"modified":"2026-11-15T09:54:13","modified_gmt":"2026-11-15T01:54:13","slug":"checkm2-prodigal-n-padding-fragmentation-features","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/checkm2-prodigal-n-padding-fragmentation-features\/","title":{"rendered":"CheckM2 \u524d\u5904\u7406\u600e\u6837\u6838\u5bf9\uff1f\u5b9e\u8dd1\u516d\u7ec4\u8f93\u5165\uff0c\u8ffd\u8e2a N\u3001\u5e8f\u5217\u5207\u5206\u4e0e\u7f16\u7801\u5bc6\u5ea6\u7684\u53d8\u5316"},"content":{"rendered":"
\n

\u505a\u57fa\u56e0\u7ec4\u8d28\u91cf\u8bc4\u4f30\u65f6\uff0c\u5b8c\u6574\u5ea6\u548c\u6c61\u67d3\u5ea6\u5f80\u5f80\u6700\u53d7\u5173\u6ce8\uff0c\u4f46\u5b83\u4eec\u524d\u9762\u8fd8\u6709\u5e8f\u5217\u8bfb\u53d6\u3001\u57fa\u56e0\u9884\u6d4b\u548c\u7279\u5f81\u8ba1\u7b97\u3002\u8f93\u5165\u4e2d\u7684\u672a\u77e5\u78b1\u57fa\u3001\u7247\u6bb5\u8fb9\u754c\u4e0e\u7ffb\u8bd1\u8868\uff0c\u4f1a\u6539\u53d8\u8fdb\u5165\u540e\u7eed\u5206\u6790\u7684\u86cb\u767d\u548c\u6570\u503c\u3002\u9047\u5230\u770b\u8d77\u6765\u5f02\u5e38\u7684\u8d28\u91cf\u7ed3\u679c\uff0c\u56de\u5230\u8fd9\u4e9b\u4e2d\u95f4\u8bc1\u636e\uff0c\u901a\u5e38\u6bd4\u53cd\u590d\u4fee\u6539\u7b5b\u9009\u95e8\u69db\u66f4\u5bb9\u6613\u627e\u5230\u539f\u56e0\u3002<\/p>\n

\u672c\u6587\u56fa\u5b9a CheckM2 1.1.0 \u7684\u5b98\u65b9\u6e90\u7801\uff0c\u5e76\u90e8\u7f72\u539f\u7248\u57fa\u56e0\u9884\u6d4b\u9636\u6bb5\u9700\u8981\u7684\u4f9d\u8d56\uff0c\u7528\u540c\u4e00\u6bb5\u53c2\u8003\u5e8f\u5217\u5236\u4f5c\u516d\u7ec4\u8f93\u5165\uff0c\u5b9e\u9645\u8fd0\u884c\u539f\u7248\u524d\u5904\u7406\u65b9\u6cd5\u3002\u5b9e\u9a8c\u8bb0\u5f55\u8986\u76d6\u57fa\u56e0\u9884\u6d4b\u3001\u5e8f\u5217\u7edf\u8ba1\u53ca\u86cb\u767d\u6838\u5bf9\u3002\u5b8c\u6574\u5ea6\u548c\u6c61\u67d3\u5ea6\u7684\u673a\u5668\u5b66\u4e60\u9884\u6d4b\uff0c\u9700\u8981\u7ee7\u7eed\u4f7f\u7528\u5339\u914d\u7684\u529f\u80fd\u6570\u636e\u5e93\u4e0e\u6a21\u578b\u6d41\u7a0b\uff0c\u672c\u6587\u7684\u5b9e\u6d4b\u6570\u503c\u5747\u6765\u81ea\u524d\u5904\u7406\u9636\u6bb5\u3002<\/p>\n

\"\u7f16\u7801\u5bc6\u5ea6\u4e0a\u5347\uff0c\u86cb\u767d\u53ef\u9760\u5417\u3002\u6838\u5bf9\u672a\u77e5\u78b1\u57fa\u4f4d\u7f6e\u548c\u9884\u6d4b\u86cb\u767d\u5185\u5bb9\u3002\u539f\u59cb
\u6838\u5bf9\u672a\u77e5\u78b1\u57fa\u4f4d\u7f6e\u548c\u9884\u6d4b\u86cb\u767d\u5185\u5bb9<\/figcaption><\/figure>\n

\u5148\u770b\u6e05\u62a5\u544a\u524d\u9762\u7684\u6570\u636e\u6d41<\/h2>\n

CheckM2 \u901a\u8fc7\u57fa\u56e0\u7ec4\u7279\u5f81\u9884\u6d4b\u5b8c\u6574\u5ea6\u548c\u6c61\u67d3\u5ea6\uff0c\u5de5\u4f5c\u6d41\u7a0b\u5305\u542b\u86cb\u767d\u9884\u6d4b\u3001\u529f\u80fd\u5339\u914d\u548c\u6a21\u578b\u8ba1\u7b97\u3002\u5b98\u65b9\u8bf4\u660e\u4e5f\u63d0\u4f9b\u4e86\u86cb\u767d\u8f93\u5165\u65b9\u5f0f\uff0c\u4ee5\u53ca\u7528\u4e8e\u68c0\u67e5\u5b89\u88c5\u548c\u6570\u636e\u5e93\u914d\u7f6e\u7684\u6d4b\u8bd5\u547d\u4ee4\u3002\u56e0\u6b64\uff0c\u6b63\u5f0f\u6bd4\u8f83\u6837\u672c\u524d\uff0c\u5e94\u5148\u660e\u786e\u8f93\u5165\u7a76\u7adf\u662f\u6838\u82f7\u9178\u5e8f\u5217\u8fd8\u662f\u5df2\u7ecf\u9884\u6d4b\u597d\u7684\u86cb\u767d\uff0c\u5e76\u8bb0\u5f55\u8f6f\u4ef6\u4e0e\u6570\u636e\u5e93\u7248\u672c\u3002CheckM2 \u5b98\u65b9\u8bf4\u660e<\/a><\/p>\n

\u672c\u6587\u5c06\u6ce8\u610f\u529b\u653e\u5728\u6838\u82f7\u9178\u8f93\u5165\u5230\u86cb\u767d\u7279\u5f81\u8fd9\u4e00\u6b65\u3002\u8fd9\u91cc\u53ef\u4ee5\u76f4\u63a5\u89c2\u5bdf\u6bcf\u4e2a\u8f93\u5165\u6709\u591a\u5c11\u78b1\u57fa\u3001\u591a\u5c11\u7247\u6bb5\u3001\u4ea7\u751f\u591a\u5c11\u86cb\u767d\uff0c\u4ee5\u53ca\u7f16\u7801\u533a\u57df\u8986\u76d6\u4e86\u591a\u5927\u6bd4\u4f8b\u3002\u5b83\u4eec\u5bf9\u8bca\u65ad\u8f93\u5165\u95ee\u9898\u5f88\u6709\u5e2e\u52a9\uff0c\u540c\u65f6\u5404\u81ea\u4e5f\u5b58\u5728\u9002\u7528\u8fb9\u754c\u3002<\/p>\n

\u4f8b\u5982\uff0c\u65b0\u589e\u672a\u77e5\u78b1\u57fa\u53ef\u80fd\u8ba9\u5e8f\u5217\u957f\u5ea6\u548c\u8fde\u7eed\u6027\u6307\u6807\u589e\u52a0\uff0c\u5374\u6ca1\u6709\u5e26\u6765\u53ef\u786e\u5b9a\u7684\u65b0\u78b1\u57fa\u4fe1\u606f\u3002\u5207\u5f00\u5df2\u6709\u5e8f\u5217\u4f1a\u589e\u52a0\u7247\u6bb5\u8fb9\u754c\uff0c\u90e8\u5206\u57fa\u56e0\u9884\u6d4b\u53ef\u80fd\u56e0\u6b64\u6539\u53d8\u3002\u82e5\u53ea\u770b\u4e00\u4e2a\u6c47\u603b\u6570\u5b57\uff0c\u5f88\u96be\u533a\u5206\u8fd9\u4e9b\u60c5\u51b5\uff0c\u4fdd\u5b58\u539f\u59cb\u5e8f\u5217\u548c\u9884\u6d4b\u86cb\u767d\u80fd\u63d0\u4f9b\u8fdb\u4e00\u6b65\u68c0\u67e5\u7684\u4f9d\u636e\u3002<\/p>\n

\u7528\u540c\u4e00\u6bb5\u53c2\u8003\u5e8f\u5217\u6784\u9020\u516d\u7ec4\u6761\u4ef6<\/h2>\n

\u5b9e\u9a8c\u4f7f\u7528\u5927\u80a0\u6746\u83cc\u53c2\u8003\u5e8f\u5217 NC_000913.3<\/code> \u7684\u524d\u5341\u4e8c\u4e07\u78b1\u57fa\uff0c\u5bf9\u5e94\u4ece\u4e00\u5f00\u59cb\u8ba1\u6570\u7684\u7b2c\u4e00\u4f4d\u5230\u7b2c\u5341\u4e8c\u4e07\u4f4d\u3002\u9009\u62e9\u56fa\u5b9a\u533a\u95f4\uff0c\u662f\u4e3a\u4e86\u8ba9\u6bcf\u4e2a\u4eba\u4e0b\u8f7d\u540c\u4e00\u6761\u53c2\u8003\u540e\uff0c\u90fd\u53ef\u4ee5\u751f\u6210\u5b8c\u5168\u4e00\u81f4\u7684\u8f93\u5165\u3002\u6240\u6709\u5bf9\u7167\u7684\u6587\u4ef6\u6821\u9a8c\u503c\u548c\u539f\u59cb\u53c2\u8003\u5e8f\u5217\u6821\u9a8c\u503c\u90fd\u5199\u5165\u7ed3\u679c\u8bb0\u5f55\u3002<\/p>\n

\u7b2c\u4e00\u7ec4\u4fdd\u7559\u539f\u59cb\u533a\u95f4\u3002\u7b2c\u4e8c\u7ec4\u53ea\u628a\u5b57\u6bcd\u8f6c\u6210\u5c0f\u5199\u3002\u7b2c\u4e09\u7ec4\u5728\u533a\u95f4\u672b\u5c3e\u8ffd\u52a0\u5341\u4e8c\u4e07\u4e2a\u672a\u77e5\u78b1\u57fa\u7b26\u53f7\u3002\u7b2c\u56db\u7ec4\u628a\u540c\u6837\u6570\u91cf\u7684\u672a\u77e5\u7b26\u53f7\u63d2\u5728\u539f\u533a\u95f4\u4e2d\u95f4\u3002\u7b2c\u4e94\u7ec4\u628a\u539f\u533a\u95f4\u5207\u6210\u516d\u5341\u6761\u4e24\u5343\u78b1\u57fa\u7247\u6bb5\u3002\u7b2c\u516d\u7ec4\u4fdd\u6301\u539f\u59cb\u5e8f\u5217\uff0c\u540c\u65f6\u5f3a\u5236\u4f7f\u7528\u7b2c\u56db\u53f7\u7ffb\u8bd1\u8868\uff0c\u4f5c\u4e3a\u53c2\u6570\u654f\u611f\u6027\u5bf9\u7167\u3002<\/p>\n

\u672c\u6b21\u524d\u5904\u7406\u4f7f\u7528 CheckM2 \u6e90\u7801\u63d0\u4ea4 f0a9eb291df899890e23542591db5c852e200c35<\/code>\u3001Prodigal 2.6.3\u3001Python 3.12 \u4e0e NumPy 1.26.4\u3002\u6700\u7ec8\u8bb0\u5f55\u6765\u81ea\u4f5c\u8005\u53d1\u5e03\u7684 Prodigal Linux \u53ef\u6267\u884c\u6587\u4ef6\u3002\u6211\u4eec\u4e5f\u6838\u5bf9\u4e86\u672c\u5730\u53d1\u884c\u5305\u7684\u76f8\u540c\u7248\u672c\uff0c\u4e24\u79cd\u53ef\u6267\u884c\u6587\u4ef6\u5728\u539f\u59cb\u533a\u95f4\u3001\u5c0f\u5199\u3001\u672b\u5c3e\u8ffd\u52a0\u672a\u77e5\u78b1\u57fa\u3001\u5207\u5206\u7247\u6bb5\u548c\u5f3a\u5236\u7ffb\u8bd1\u8868\u4e94\u4e2a\u6761\u4ef6\u4e0b\u5f97\u5230\u76f8\u540c\u7edf\u8ba1\u7ed3\u679c\u3002\u672c\u6b21 CheckM2 \u524d\u5904\u7406\u5b9e\u73b0<\/a>\u3001Prodigal \u7248\u672c\u53d1\u5e03\u9875<\/a><\/p>\n

\u8fd0\u884c\u811a\u672c\u63a5\u6536\u6e90\u7801\u76ee\u5f55\u3001\u53c2\u8003\u5e8f\u5217\u548c\u8f93\u51fa\u76ee\u5f55\uff0c\u968f\u540e\u76f4\u63a5\u8c03\u7528\u539f\u7248\u65b9\u6cd5\u3002\u8f93\u5165\u4e0e\u8f93\u51fa\u5206\u522b\u653e\u5728\u72ec\u7acb\u76ee\u5f55\uff0c\u907f\u514d\u9884\u6d4b\u4ea7\u751f\u7684\u4e2d\u95f4\u6587\u4ef6\u4e0e\u539f\u59cb\u5e8f\u5217\u4f7f\u7528\u540c\u4e00\u4e2a\u4f4d\u7f6e\u3002<\/p>\n

from checkm2.prodigal import ProdigalRunner\r\n\r\nrunner = ProdigalRunner("work\/original", "input\/original.fna")\r\nfeatures = runner.run("input\/original.fna")\r\nprint(features)\r\n<\/code><\/pre>\n
\u5148\u770b\u516d\u6b21\u8fd0\u884c\u7559\u4e0b\u7684\u6570\u5b57<\/h2>\n
\u539f\u59cb\u533a\u95f4\u4ea7\u751f\u4e00\u767e\u96f6\u56db\u6761\u9884\u6d4b\u86cb\u767d\uff0c\u7f16\u7801\u5bc6\u5ea6\u7ea6\u4e3a\u767e\u5206\u4e4b\u516b\u5341\u4e5d\u70b9\u516b\u4e8c\u3002\u8f6c\u4e3a\u5c0f\u5199\u4ee5\u540e\uff0c\u86cb\u767d\u6570\u91cf\u3001\u957f\u5ea6\u7edf\u8ba1\u548c\u7f16\u7801\u5bc6\u5ea6\u5b8c\u5168\u76f8\u540c\uff0c\u6392\u5e8f\u540e\u7684\u86cb\u767d\u5e8f\u5217\u96c6\u5408\u6821\u9a8c\u503c\u4e5f\u76f8\u540c\u3002\u8fd9\u8bf4\u660e\u5728\u672c\u6b21\u7248\u672c\u4e0e\u8f93\u5165\u4e0a\uff0c\u5927\u5c0f\u5199\u53d8\u5316\u6ca1\u6709\u6539\u53d8\u9884\u6d4b\u86cb\u767d\u5185\u5bb9\u3002<\/p>\n
\n\n\n\n\n\n\n\n\n\n\n
\u8f93\u5165\u6761\u4ef6<\/th>\n\u603b\u78b1\u57fa\u6570<\/th>\n\u660e\u786e\u78b1\u57fa\u6570<\/th>\n\u9884\u6d4b\u86cb\u767d\u6570<\/th>\n\u7f16\u7801\u5bc6\u5ea6<\/th>\nN50<\/th>\n<\/tr>\n<\/thead>\n
\u539f\u59cb\u533a\u95f4<\/td>\n120,000<\/td>\n120,000<\/td>\n104<\/td>\n89.8208%<\/td>\n120,000<\/td>\n<\/tr>\n
\u8f6c\u6210\u5c0f\u5199<\/td>\n120,000<\/td>\n120,000<\/td>\n104<\/td>\n89.8208%<\/td>\n120,000<\/td>\n<\/tr>\n
\u672b\u5c3e\u8ffd\u52a0 N<\/td>\n240,000<\/td>\n120,000<\/td>\n105<\/td>\n94.8854%<\/td>\n240,000<\/td>\n<\/tr>\n
\u4e2d\u95f4\u63d2\u5165 N<\/td>\n240,000<\/td>\n120,000<\/td>\n152<\/td>\n47.5658%<\/td>\n240,000<\/td>\n<\/tr>\n
\u5207\u6210 2 kb \u7247\u6bb5<\/td>\n120,000<\/td>\n120,000<\/td>\n155<\/td>\n90.1692%<\/td>\n2,000<\/td>\n<\/tr>\n
\u5f3a\u5236\u7b2c\u56db\u53f7\u7ffb\u8bd1\u8868<\/td>\n120,000<\/td>\n120,000<\/td>\n102<\/td>\n90.0258%<\/td>\n120,000<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u8fd9\u5f20\u8868\u4e2d\u6700\u503c\u5f97\u7ee7\u7eed\u68c0\u67e5\u7684\u662f\u8ffd\u52a0\u672a\u77e5\u7b26\u53f7\u7684\u4e00\u7ec4\u3002\u5b83\u62e5\u6709\u66f4\u5927\u7684\u957f\u5ea6\u3001\u66f4\u9ad8\u7684\u8fde\u7eed\u6027\u6307\u6807\uff0c\u7f16\u7801\u5bc6\u5ea6\u751a\u81f3\u4e0a\u5347\u4e86\u4e94\u4e2a\u591a\u767e\u5206\u70b9\u3002\u4ec5\u51ed\u8fd9\u4e9b\u6570\u5b57\uff0c\u5f88\u5bb9\u6613\u4ea7\u751f\u8f93\u5165\u6539\u5584\u4e86\u7684\u5370\u8c61\u3002\u660e\u786e\u78b1\u57fa\u6570\u91cf\u4ecd\u4e3a\u5341\u4e8c\u4e07\uff0c\u63d0\u793a\u6211\u4eec\u9700\u8981\u68c0\u67e5\u65b0\u589e\u52a0\u7684\u9884\u6d4b\u533a\u57df\u5230\u5e95\u662f\u4ec0\u4e48\u3002<\/p>\n
\u8ffd\u5230\u86cb\u767d\u6587\u4ef6\uff0c\u627e\u5230\u56db\u4e07\u4e2a\u672a\u77e5\u6c28\u57fa\u9178<\/h2>\n
\u6253\u5f00\u672b\u5c3e\u8ffd\u52a0\u672a\u77e5\u78b1\u57fa\u90a3\u4e00\u7ec4\u7684\u86cb\u767d\u7ed3\u679c\uff0c\u53ef\u4ee5\u627e\u5230\u4e00\u6761\u957f\u8fbe\u56db\u4e07\u96f6\u4e8c\u767e\u56db\u5341\u4f4d\u7684\u9884\u6d4b\u86cb\u767d\uff0c\u5176\u4e2d\u56db\u4e07\u4f4d\u662f\u672a\u77e5\u6c28\u57fa\u9178\u7b26\u53f7\u3002\u5bf9\u5e94\u9884\u6d4b\u533a\u95f4\u5ef6\u4f38\u5230\u4e86\u8f93\u5165\u672b\u7aef\uff0c\u628a\u8ffd\u52a0\u533a\u57df\u7eb3\u5165\u4e86\u8fd9\u6761\u9884\u6d4b\u8bb0\u5f55\u3002<\/p>\n
\u539f\u59cb\u7ec4\u6700\u957f\u86cb\u767d\u4e3a\u4e00\u5343\u96f6\u4e03\u5341\u56db\u4f4d\uff0c\u86cb\u767d\u4e2d\u6ca1\u6709\u672a\u77e5\u6c28\u57fa\u9178\u3002\u8fd9\u4e2a\u5bf9\u7167\u8ba9\u5f02\u5e38\u53d8\u5f97\u5177\u4f53\u3002\u7f16\u7801\u5bc6\u5ea6\u63d0\u9ad8\u7684\u540c\u65f6\uff0c\u51fa\u73b0\u4e86\u4e00\u6761\u7531\u5927\u91cf\u672a\u77e5\u6b8b\u57fa\u6784\u6210\u7684\u6781\u957f\u86cb\u767d\u3002\u8fdb\u5165\u540e\u7eed\u5206\u6790\u4e4b\u524d\uff0c\u5e94\u7ed3\u5408\u8fd9\u6761\u8bb0\u5f55\u53ca\u5176\u6765\u6e90\uff0c\u91cd\u65b0\u5224\u65ad\u5bc6\u5ea6\u6570\u503c\u6240\u53cd\u6620\u7684\u5177\u4f53\u5185\u5bb9\u3002<\/p>\n
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\u600e\u6837\u628a\u86cb\u767d\u68c0\u67e5\u52a0\u5165\u81ea\u5df1\u7684\u5206\u6790<\/h2>\n
\u53ef\u4ee5\u5148\u8ba1\u7b97\u6bcf\u6761\u86cb\u767d\u7684\u957f\u5ea6\u3001\u672a\u77e5\u6b8b\u57fa\u6570\u548c\u672a\u77e5\u6b8b\u57fa\u6bd4\u4f8b\uff0c\u518d\u628a\u6781\u7aef\u503c\u6309\u957f\u5ea6\u6216\u6bd4\u4f8b\u6392\u5e8f\u67e5\u770b\u3002\u8fd9\u91cc\u7684\u9608\u503c\u5e94\u6839\u636e\u6570\u636e\u7c7b\u578b\u548c\u7814\u7a76\u5bf9\u8c61\u786e\u5b9a\u3002\u5bf9\u6559\u5b66\u4f8b\u5b50\u800c\u8a00\uff0c\u4e00\u6761\u56db\u4e07\u591a\u4f4d\u3001\u51e0\u4e4e\u5168\u90e8\u7531\u672a\u77e5\u6b8b\u57fa\u7ec4\u6210\u7684\u8bb0\u5f55\uff0c\u5df2\u7ecf\u8db3\u4ee5\u5b9a\u4f4d\u5230\u9700\u8981\u68c0\u67e5\u7684\u8f93\u5165\u533a\u57df\u3002<\/p>\n
from Bio import SeqIO\r\n\r\nfor record in SeqIO.parse("predicted.faa", "fasta"):\r\n    protein = str(record.seq)\r\n    unknown = protein.count("X")\r\n    fraction = unknown \/ len(protein) if protein else 0\r\n    if unknown:\r\n        print(record.id, len(protein), unknown, fraction, sep="\\t")\r\n<\/code><\/pre>\n
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\u7ffb\u8bd1\u8868\u9009\u62e9\u8981\u6709\u751f\u7269\u5b66\u4f9d\u636e<\/h2>\n
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