{"id":61308,"date":"2024-10-28T15:26:13","date_gmt":"2024-10-28T07:26:13","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61308"},"modified":"2024-10-28T15:26:13","modified_gmt":"2024-10-28T07:26:13","slug":"%e5%8f%aa%e4%bc%9a%e7%94%a8ncbi%e5%8e%bbblast%ef%bc%9f%e5%a4%9a%e5%ba%8f%e5%88%97%e6%af%94%e5%af%b9%e7%a5%9e%e5%99%a8mafft%e4%b8%80%e7%ab%99%e5%bc%8f%e8%a7%a3%e5%86%b3%e4%bd%a0%e7%9a%84%e5%ba%8f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61308","title":{"rendered":"\u53ea\u4f1a\u7528NCBI\u53bbblast\uff1f\u591a\u5e8f\u5217\u6bd4\u5bf9\u795e\u5668mafft\u4e00\u7ad9\u5f0f\u89e3\u51b3\u4f60\u7684\u5e8f\u5217\u6bd4\u5bf9\u96be\u9898\uff01\u4eb2\u6d4b\u6709\u6548\uff0c\u7b80\u5355\u8be6\u7ec6"},"content":{"rendered":"\n

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

\"\"<\/figure>\n\n\n\n

Hi\uff01\u8fd9\u91cc\u662f\u5c0f\u5e08\u59b9\u3002\u8fd8\u8bb0\u5f97\u672c\u79d1\u4e0a\u8bfe\u65f6\u8001\u5e08\u62ff\u7740\u7cfb\u7edf\u8fdb\u5316\u5206\u6790\u5ffd\u60a0\u4f60\uff0c\u4f1a\u7528MEGA\u5417\uff1f\u53c8\u6216\u662f\u5728Windows\u4e0a\u4e00\u901a\u64cd\u4f5cMega\u8f6f\u4ef6\uff0c\u529f\u80fd\u867d\u591a\u4f46\u7e41\u6742\uff0c\u800c\u4e14\u8fd0\u884c\u901f\u5ea6\u8fd8\u5f88\u53d7\u9650\u4e8e\u672c\u5730\u7535\u8111\u7684\u914d\u7f6e\uff0c\u4eca\u5929\u5c0f\u5e08\u59b9\u5c31\u7ed9\u5927\u5bb6\u5e26\u6765\u5220\u7e41\u5c31\u7b80\u7248\u7684\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\uff0c\u6700\u5927\u7a0b\u5ea6\u51cf\u8f7b\u5c0f\u767d\u7684\u70e6\u607c\uff0c\u8d76\u7d27\u62ff\u8d77\u5c0f\u672c\u672c\u8bb0\u597d\uff01<\/p>\n\n\n\n

\u8fd9\u4e2a\u8f6f\u4ef6\u652f\u6301\u591a\u79cd\u6bd4\u5bf9\u7b97\u6cd5\uff0c\u5305\u62ecFFT+NS+2\u3001FFT+NS+i\u3001FFT+NS+1\u3001L+INS+i\u3001G+INS+i\u548cE+INS+i\u7b49\u7b49\u3002\u91cd\u8981\u7684\u662f\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u9700\u6c42\u9009\u62e9\u4e0d\u540c\u7684\u7b97\u6cd5\u8fdb\u884c\u6bd4\u5bf9\uff0c\u800c\u4e14\u5c31\u7b97\u4f60\u4e0d\u4f1a\uff0c\u6a21\u578b\u8fd8\u4f1a\u5e2e\u4f60\u9009\u62e9\u6700\u4f73\u6a21\u578b\u54e6~\u672c\u6b21\u4ecb\u7ecd\u7684\u8f6f\u4ef6\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u5e08\u59b9\u79df\u8d41\u6027\u4ef7\u6bd4\u5c45\u9ad8\u7684\u670d\u52a1\u5668~<\/strong><\/p>\n\n\n\n

\u5f53\u7136\u6211\u4eec\u4e0d\u80fd\u53ea\u9650\u4e8e\u5bf9\u8f6f\u4ef6\u7684\u4f7f\u7528\uff0c\u8fd8\u8981\u4e86\u89e3\u8f6f\u4ef6\u539f\u7406\u624d\u80fd\u6e38\u5203\u6709\u4f59\uff0c\u4e0d\u88ab\u5668\u5177\u6240\u652f\u914d\u3002\u4eca\u5929\u5c0f\u5e08\u59b9\u5219\u7ed9\u5927\u5bb6\u5e26\u6765\u591a\u5e8f\u5217\u6bd4\u5bf9\u795e\u5668mafft\u5de5\u5177\u7684\u5206\u6790\u3002\u5b83\u4e0d\u4ec5\u5feb\u901f\u3001\u9ad8\u6548\u3001\u51c6\u786e\uff0c\u652f\u6301\u591a\u79cd\u64cd\u4f5c\u7cfb\u7edf\uff0c\u5305\u62ecWindows\u3001Linux\u548cMac OS\u7b49,\u800c\u4e14\u53ef\u4ee5\u540c\u65f6\u5904\u7406\u5927\u91cf\u7684\u5e8f\u5217\u6570\u636e\uff0c\u5e76\u751f\u6210\u9ad8\u8d28\u91cf\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u63a5\u4e0b\u6765\uff0c\u540c\u5b66\u4eec\u8ddf\u7d27\u5c0f\u5e08\u59b9\u7684\u6b65\u4f10\uff0c\u8ba9\u6211\u4eec\u6b63\u5f0f\u5f00\u542f\u5bf9Mafft\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01 \u5982\u679c\u4f60\u5728\u64cd\u4f5c\u8fc7\u7a0b\u4e2d\u9047\u5230\u4efb\u4f55\u95ee\u9898\uff0c\u522b\u72b9\u8c6b\uff0c\u8bb0\u5f97\u8054\u7cfb\u5c0f\u5e08\u59b9\u54e6~<\/strong><\/strong><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u4e00\u3001\u4ec0\u4e48\u662fMafft\uff1f<\/strong><\/strong><\/p>\n\n\n\n

\u4e00\u63d0\u5230\u591a\u91cd\u5e8f\u5217\u6bd4\u5bf9\uff0c\u5f88\u591a\u4eba\u7981\u4e0d\u4f4f\u5c31\u60f3\u5230ClustalW\uff0c\u800c\u5bf9\u4e8e\u51e0\u5343\u6761\u5e8f\u5217\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\uff0c\u65e0\u8bba\u662f\u4ece\u51c6\u786e\u5ea6\u8fd8\u662f\u8fd0\u884c\u901f\u5ea6\u4e0a\u8003\u8651\uff0cmuscle\u901a\u5e38\u90fd\u662f\u6700\u4f73\u9009\u62e9\u3002\u4f46\u662fmuscle\u7684\u5185\u5b58\u4f18\u5316\u505a\u7684\u5e76\u4e0d\u597d\uff0c\u5982\u679c\u6240\u9700\u5185\u5b58\u8d85\u51fa\u4e86\u673a\u5668\u5185\u5b58\uff0c\u6b64\u65f6\u53ef\u4ee5\u8003\u8651mafft\u8fd9\u4e2a\u5de5\u5177\u3002<\/p>\n\n\n\n

MAFFT\u5168\u79f0\u662fMultiple Alignment using Fast Fourier Transform\uff0c\u8d77\u521d\u662f\u4e3a\u4e86\u6267\u884c\u5927\u89c4\u6a21\u5e8f\u5217\u6bd4\u5bf9\u800c\u53d1\u5c55\u8d77\u6765\u7684\uff0c\u5b83\u662f\u4e00\u79cd\u57fa\u4e8e\u5feb\u901f\u5085\u91cc\u53f6\u53d8\u6362\u7684\u7ec4\u5bf9\u7ec4\u7684\u6bd4\u5bf9\u7b97\u6cd5\uff0c\u5e76\u4e14\u4f7f\u7528\u4e86\u4e00\u79cd\u8fd1\u4f3c\u8ddd\u79bb\u8ba1\u7b97\u65b9\u6cd5\u4fbf\u4e8e\u8fdb\u884c\u5feb\u901f\u8ba1\u7b97\u3002<\/p>\n\n\n\n

\u80cc\u666f\u77e5\u8bc6\uff1a\u5085\u91cc\u53f6\u53d8\u6362\u539f\u7406\u5373\u4efb\u4f55\u4e00\u4e2a\u590d\u6742\u7684\u6ce2\u90fd\u53ef\u4ee5\u62c6\u89e3\u6210\u8bb8\u591a\u4e2asine\uff08wave\uff09\uff0c\u628a\u4e00\u4e2a\u590d\u6742\u7684\u6ce2\u8f6c\u5316\u6210\u4e3a\u591a\u4e2a\u6807\u51c6\u6b63\u5f26\u6ce2\u53e0\u52a0\u7684\u8fc7\u7a0b\u5c31\u662f\u5085\u91cc\u53f6\u53d8\u6362\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe1 \u5de5\u5177\u5f15\u7528\u60c5\u51b5<\/p>\n\n\n\n

\u4e8c\u3001\u4e0b\u8f7d\u548c\u5b89\u88c5<\/strong><\/strong><\/h1>\n\n\n\n

mafft \u662f\u4e00\u4e2a\u8de8\u5e73\u53f0\u7684\u5de5\u5177\uff0cMAFFT\u5b98\u65b9\u7f51\u7ad9\uff1ahttp:\/\/mafft.cbrc.jp\/alignment\/software\/\uff0c\u652f\u6301\u5e73\u53f0\uff1aMac OS X \u3001Linux\u3001Windows\u3002\u4e0b\u9762\u7ed9\u5927\u5bb6\u5e26\u6765linux\u7cfb\u7edf\u7684\u5b89\u88c5\uff0c\u9700\u8981\u6839\u636e\u81ea\u5df1\u64cd\u4f5c\u7cfb\u7edf\u9009\u62e9\u76f8\u5e94\u7248\u672c\u4e0b\u8f7d\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe2 Mafft\u5de5\u5177\u5b98\u7f51<\/p>\n\n\n\n

\u7b2c\u4e00\u6b65\uff1a\u4e0b\u8f7d\u5b89\u88c5\u5305<\/strong><\/p>\n\n\n\n

$ wget -c https:\/\/mafft.cbrc.jp\/alignment\/software\/mafft-7.520-linux.tgz<\/strong><\/strong><\/p>\n\n\n\n

\u7b2c\u4e8c\u6b65\uff1a\u89e3\u538b<\/strong><\/p>\n\n\n\n

$ tar -zxvf mafft-7.520-linux.tgz<\/strong><\/strong><\/p>\n\n\n\n

\u7b2c\u4e09\u6b65\uff1a\u6539\u540d<\/strong><\/strong><\/p>\n\n\n\n

$ mv mafft-linux64 mafft<\/strong><\/strong><\/p>\n\n\n\n

$ cd mafft<\/strong><\/strong><\/p>\n\n\n\n

$ chmod a+x .\/mafft.bat<\/strong><\/strong><\/p>\n\n\n\n

$ mv mafft.bat mafft<\/strong><\/strong><\/p>\n\n\n\n

\u4e09\u3001<\/strong>\u5e38\u89c1\u547d\u4ee4<\/strong><\/strong><\/h1>\n\n\n\n

1.\u57fa\u672c\u6bd4\u5bf9\u547d\u4ee4<\/strong><\/strong><\/p>\n\n\n\n

\u8f93\u5165\u5e8f\u5217\u7684\u7c7b\u578b(\u6c28\u57fa\u9178\u6216\u6838\u82f7\u9178)\u662f\u81ea\u52a8\u8bc6\u522b\u7684<\/p>\n\n\n\n

$ mafft  sample1.fasta > sample1.output.fasta<\/strong><\/strong><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe3 \u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n

\u6309\u7167\u6700\u957f\u5e8f\u5217\uff0c\u628a\u76f8\u5e94\u4f4d\u7f6e\u7684aa\u6807\u51fa\u6765\uff0c\u6709gap\u7684\u5730\u65b9\uff0c\u5219\u7528—\u8865\u9f50\u3002<\/p>\n\n\n\n

2.\u8fed\u4ee3\u6bd4\u5bf9<\/strong><\/p>\n\n\n\n

\u6700\u5927\u8fed\u4ee3\u6b21\u6570–maxiterate\uff0c\u8fd9\u91cc\u4f7f\u7528\u4e86–maxiterate\u8bbe\u7f6e\u6700\u5927\u8fed\u4ee3\u6b21\u6570\u548c–localpair\u6bd4\u5bf9\u7b56\u7565\u8fdb\u884c\u5c40\u90e8\u6bd4\u5bf9\u3002<\/p>\n\n\n\n

$ mafft –maxiterate 1000 –localpair input.fasta > output.fasta<\/strong><\/strong><\/p>\n\n\n\n

3.\u6bd4\u5bf9\u7b56\u7565<\/strong><\/p>\n\n\n\n

mafft \u652f\u6301\u6838\u9178\u548c\u86cb\u767d\u5e8f\u5217\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\uff0c\u5e76\u5185\u7f6e\u4e86\u591a\u79cd\u5e8f\u5217\u6bd4\u5bf9\uff0c\u8fd9\u91cc\u4e3b\u8981\u4ecb\u7ecdHigh accuracy\u4e2d\u7684\u4e09\u79cd\u6bd4\u5bf9\u65b9\u6cd5\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe4 Mafft\u5e2e\u52a9\u6587\u6863<\/p>\n\n\n\n

1\uff09L-INS-I\uff1a\u6700\u51c6\u786e\u7684\u65b9\u6cd5\uff0c\u9002\u5408\u5c0f\u4e8e200\u6761\uff0c\u4e14\u957f\u5ea6\u5c0f\u4e8e2000aa\/nt\u7684\u5e8f\u5217\u3002<\/p>\n\n\n\n

$ mafft –maxiterate 1000 –localpair input > output<\/strong><\/strong><\/p>\n\n\n\n

2\uff09G-INS-I\uff1a\u9002\u5408\u5e8f\u5217\u957f\u5ea6\u76f8\u4f3c\u7684\u6bd4\u5bf9\uff0c\u5c0f\u4e8e200\u6761\uff0c\u4e14\u957f\u5ea6\u5c0f\u4e8e2000aa\/nt\u7684\u5e8f\u5217\u3002<\/p>\n\n\n\n

$ mafft –maxiterate 1000 –globalpair input > output<\/strong><\/strong><\/p>\n\n\n\n

3\uff09E-INS-I\uff1a\u9002\u5408\u5e8f\u5217\u4e2d\u5305\u542b\u8f83\u5927\u7684\u975e\u5339\u914d\u533a\u57df\uff0c\u5c0f\u4e8e200\u6761\uff0c\u4e14\u957f\u5ea6\u5c0f\u4e8e2000aa\/nt\u7684\u5e8f\u5217<\/p>\n\n\n\n

$ mafft –maxiterate 1000 –genafpair input > output<\/strong><\/strong><\/p>\n\n\n\n

4.\u81ea\u52a8\u9009\u62e9\u6bd4\u5bf9\u7b56\u7565<\/strong><\/p>\n\n\n\n

\u524d\u9762\u8bb2\u4e86\u8fd9\u4e48\u591a\u7684\u7b56\u7565\uff0c\u662f\u4e0d\u662f\u89c9\u5f97\u6709\u70b9\u61f5\u4e86\uff1f\u6ca1\u5173\u7cfb\uff0c\u8fd9\u91cc\u8fd8\u53ef\u4ee5\u9009\u62e9\u81ea\u52a8\u6bd4\u5bf9\u7b56\u7565\uff0c\u4f7f\u7528–auto\u9009\u9879\uff0cMAFFT\u4f1a\u6839\u636e\u8f93\u5165\u5e8f\u5217\u7684\u5927\u5c0f\u548c\u6570\u91cf\u81ea\u52a8\u9009\u62e9\u6700\u5408\u9002\u7684\u6bd4\u5bf9\u7b56\u7565\u3002<\/p>\n\n\n\n

$ mafft –auto input.fasta > output.fasta<\/strong><\/strong><\/p>\n\n\n\n

5.\u8c03\u6574\u7ebf\u7a0b\u6570\u4ee5\u52a0\u5feb\u6bd4\u5bf9\u901f\u5ea6<\/strong><\/p>\n\n\n\n

\u6211\u4eec\u8fd8\u53ef\u4ee5\u4f7f\u7528–thread\u9009\u9879\u53ef\u4ee5\u6307\u5b9a\u7ebf\u7a0b\u6570\uff0c\u4ee5\u5e76\u884c\u5904\u7406\u6765\u52a0\u5feb\u6bd4\u5bf9\u901f\u5ea6\uff0c\u4f46\u662f\u7ebf\u7a0b\u6570\u548c\u6bd4\u5bf9\u901f\u5ea6\u5e76\u4e0d\u662f\u7ebf\u6027\u9012\u589e\u5173\u7cfb\uff0c\u5b58\u5728\u4e00\u4e2a\u6700\u4f73\u6027\u80fd\u7ebf\u7a0b\u6570\uff0c\u5982\u679c\u6709\u6279\u91cf\u8dd1\u591a\u5e8f\u5217\u6bd4\u5bf9\u9700\u6c42\u7684\u4f19\u4f34\uff0c\u53ef\u4ee5\u53bb\u4e86\u89e3\u4e00\u4e0b\u3002<\/p>\n\n\n\n

$ mafft –thread 24 input.fasta > output.fasta<\/strong><\/strong><\/p>\n\n\n\n

\u56db\u3001<\/strong>\u5c0f\u7ed3<\/strong><\/strong><\/h1>\n\n\n\n

\u6700\u7ec8\u8f93\u51fa\u7684\u6587\u4ef6\u683c\u5f0f\u8fd8\u662ffasta\u6587\u4ef6\u683c\u5f0f\uff0c\u81f3\u6b64\uff0c\u5c31\u5b8c\u6210\u4e86mafft\u591a\u5e8f\u5217\u6bd4\u5bf9\u3002\u540e\u7eed\u6211\u4eec\u53ef\u4ee5\u5c06\u7ed3\u679c\u6587\u4ef6\u5bfc\u5165\u5230mega\u8fdb\u884c\u53ef\u89c6\u5316\u548c\u4fee\u526a\uff0c\u5bfc\u51fa\u6210phy\u683c\u5f0f\uff0c\u5373\u53ef\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u6811\u7684\u6784\u5efa\u5566\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe5 \u5bf9\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6\u5bfc\u5165Mega\u8f6f\u4ef6\u8fdb\u884c\u53ef\u89c6\u5316<\/p>\n\n\n\n

\u5982\u679c\u5c0f\u4f19\u4f34\u7528\u7684\u662f\u81ea\u5df1\u7684\u53f0\u5f0f\u7535\u8111\uff0c\u4e0d\u80fd\u8fdb\u884c\u5927\u4efb\u52a1\u91cf\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\uff0cEBI\u4e5f\u63d0\u4f9b\u4e86mafft\u7684\u5728\u7ebf\u670d\u52a1\uff0c\u7f51\u5740\u5982\u4e0b\uff1a<\/p>\n\n\n\n

\nhttps:\/\/www.ebi.ac.uk\/Tools\/msa\/mafft\/\n<\/div><\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n

\u56fe6 EBI\u5b98\u7f51Mafft\u5728\u7ebf\u5de5\u5177<\/p>\n\n\n\n

\u5f53\u7136\uff0c\u5e02\u9762\u4e0a\u8fd8\u6709\u5f88\u591a\u5176\u4ed6\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u8f6f\u4ef6\uff0c\u6709\u6587\u732e\u5bf9\u591a\u79cd\u591a\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\u8fdb\u884c\u4e86\u6bd4\u8f83\uff1a\u6bd4\u5bf9\u901f\u5ea6Muscle>MAFFT>ClustalW>T-Coffee\uff0c\u6bd4\u5bf9\u51c6\u786e\u6027MAFFT>Muscle>T-Coffee>ClustalW\u3002\u56e0\u6b64\uff0c\u63a8\u8350\u4f7f\u7528 MAFFT \u8f6f\u4ef6\u8fdb\u884c\u591a\u5e8f\u5217\u6bd4\u5bf9\u3002<\/p>\n\n\n\n

\u603b\u7684\u6765\u8bf4\uff0cMAFFT \u9002\u5408\u5927\u89c4\u6a21\u57fa\u56e0\u7ec4\u9879\u76ee\u3001\u591a\u6837\u5316\u7684\u6570\u636e\u96c6\u6bd4\u5bf9\uff0c\u4ee5\u53ca\u9700\u8981\u7075\u6d3b\u7b97\u6cd5\u9009\u62e9\u7684\u7814\u7a76\uff0c\u7531\u4e8e\u53c2\u6570\u4f17\u591a\uff0c\u65b0\u624b\u53ef\u80fd\u9700\u8981\u65f6\u95f4\u5b66\u4e60\u5982\u4f55\u6709\u6548\u4f7f\u7528\uff0c\u4e0d\u8fc7\u6211\u4eec\u4e5f\u53ef\u4ee5\u201c\u50bb\u74dc\u5f0f\u201d\u9009\u62e9auto\u53c2\u6570\uff0c\u4e00\u952e\u89e3\u51b3\u6240\u6709\u70e6\u607c~<\/p>\n\n\n\n

\u65e2\u7136\u8bf4\u5230\u5efa\u6811\u57fa\u4e8e\u591a\u5e8f\u5217\u6bd4\u5bf9\uff0c\u5c31\u4e0d\u5f97\u4e0d\u4ecb\u7ecd\u4e00\u4e0b\u6574\u4f53\u6d41\u7a0b\uff1a<\/p>\n\n\n\n

\u2460\u6311\u9009\u5408\u9002\u7684\u57fa\u56e0\u751f\u6210fasta\u6587\u4ef6\uff08DNA\/AA\uff09<\/p>\n\n\n\n

\u2461\u591a\u5e8f\u5217\u6bd4\u5bf9 (Mafft\/ ClustalW)<\/p>\n\n\n\n

\u2462\u53bb\u6389\u6bd4\u5bf9\u4e2d\u7684gap (TrimAl)<\/p>\n\n\n\n

\u2463\u8f6c\u6362\u683c\u5f0f\uff0c\u751f\u6210\u7684FASTA, NEXUS, CLUSTALW\u683c\u5f0f\u7684\u6587\u4ef6\u5747<\/p>\n\n\n\n

\u2464\u5efa\u6811 (IQ-TREE)<\/p>\n\n\n\n

\u2465\u8fdb\u5316\u6811\u7f8e\u5316\uff08figtree\u3001itol\u3001mega\uff09<\/p>\n\n\n\n

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