{"id":1818,"date":"2013-09-03T09:54:27","date_gmt":"2013-09-03T01:54:27","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1818"},"modified":"2013-09-06T11:51:34","modified_gmt":"2013-09-06T03:51:34","slug":"orthomcl%e7%9a%84%e8%bf%90%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1818","title":{"rendered":"OrthoMCL\u7684\u4f7f\u7528"},"content":{"rendered":"

\u520613\u6b65\u8fdb\u884c\uff0c\u5982\u4e0b\uff1a<\/p>\n

1. \u5b89\u88c5\u548c\u914d\u7f6e\u6570\u636e\u5e93<\/h1>\n

Orthomcl\u53ef\u4ee5\u4f7f\u7528Oracle\u548cMysql\u6570\u636e\u5e93\uff0c\u800c\u5728\u8fd9\u91cc\u53ea\u4ecb\u7ecd\u4f7f\u7528Mysql\u6570\u636e\u5e93\u3002
\n\u4fee\u6539\u914d\u7f6e\u6587\u4ef6\/etc\/my.cnf\uff0c\u5bf9Mysql\u8fdb\u884c\u5982\u4e0b\u914d\u7f6e\uff1a<\/p>\n

\r\n1. \u8bbe\u7f6emyisam_sort_buffer_size\u7684\u503c\u4e3a\u53ef\u7528\u5185\u5b58\u7684\u4e00\u534a\uff1b\r\n2. \u8bbe\u7f6emyisam_max_sort_file_size\u4e3aorthomclBlastParser\u7a0b\u5e8f\u751f\u6210\u6587\u4ef6similarSequences.txt\u76845\u500d\u5927\u5c0f\uff1b\r\n3. \u8f6f\u4ef6\u7684\u8bf4\u660e\u6587\u6863\u4e2d\u8bbe\u7f6eread_buffer_size\u7684\u503c\u4e3a???,\u4f46\u662f\u8bbe\u7f6e\u4e3a3\u4e2a\u95ee\u53f7\u62161\u4e2a\u95ee\u53f7\uff0c\u5219mysql\u542f\u52a8\u4e0d\u4e86\u3002\u6211\u5c06\u5176\u8bbe\u7f6e\u4e3a2000M\u3002\r\n<\/pre>\n
2. \u5b89\u88c5mcl\u8f6f\u4ef6<\/h2>\n
mcl\uff0c\u5373Markov Clustering algorithm\uff0c\u5176\u6700\u65b0\u7684\u8f6f\u4ef6\u4e0b\u8f7d\u5730\u5740\uff1ahttp:\/\/www.micans.org\/mcl\/src\/mcl-latest.tar.gz<\/a>\u3002\u4e0b\u8f7d\u540e\u4f7f\u7528’.\/configure && make && make install’\u5b89\u88c5\u5373\u53ef\u3002<\/p>\n
3. \u5b89\u88c5\u5e76\u914d\u7f6eOrthoMCL\u8f6f\u4ef6<\/h1>\n
\u4e0b\u8f7dOrthoMCL\u8f6f\u4ef6\uff08http:\/\/orthomcl.org\/common\/downloads\/software\/<\/a>\uff09\u540e\uff0c\u89e3\u538b\u7f29\u540e\uff0c\u5176\u4e2d\u5305\u542b\u6587\u4ef6\u5939:bin\u3001config\u3001doc\u3001lib\u56db\u4e2a\u6587\u4ef6\u5939\u3002
\n\u5728\u4e00\u4e2a\u5de5\u4f5c\u76ee\u5f55\u4e2d\u8fd0\u884cOrthoMCL\uff0c\u8be5\u76ee\u5f55\u5305\u542b\u6570\u636e\u6587\u4ef6\u548c\u7ed3\u679c\u6587\u4ef6\u3002\u5c06doc\/OrthoMCLEngine\/Main\/orthomcl.config.template\u590d\u5236\u5230\u5de5\u4f5c\u76ee\u5f55\u4e2d\u3002\u8be5\u6587\u4ef6\u4e3aOrthoMCL\u7684\u914d\u7f6e\u6587\u4ef6\uff0c\u4ee5\u4f7f\u7528mysql\u6570\u636e\u5e93\u4e3a\u4f8b\uff0c\u5176\u4e2d\u7684\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n
\r\ndbVendor=mysql   #\u4f7f\u7528\u7684\u6570\u636e\u5e93\u4e3amysql\r\ndbConnectString=dbi:mysql:orthomcl   #\u4f7f\u7528mysql\u6570\u636e\u5e93\u4e2d\u540d\u4e3aorthomcl\u7684\u6570\u636e\u5e93\r\ndbLogin=test    #\u6570\u636e\u5e93\u7684\u7528\u6237\u540d\r\ndbPassword=123  #\u76f8\u5e94\u7684\u5bc6\u7801\r\nsimilarSequencesTable=SimilarSequences #\r\northologTable=Ortholog\r\ninParalogTable=InParalog\r\ncoOrthologTable=CoOrtholog\r\ninterTaxonMatchView=InterTaxonMatch\r\npercentMatchCutoff=50\r\nevalueExponentCutoff=-5\r\noracleIndexTblSpc=NONE\r\n<\/pre>\n
4. \u5b89\u88c5orthomcl\u6570\u636e\u5e93\u7684\u8868<\/h1>\n
\u9996\u5148\uff0c\u8fdb\u5165mysql\u6570\u636e\u5e93\uff0c\u65b0\u5efa\u4e00\u4e2a\u540d\u4e3aorthomcl\u7684\u6570\u636e\u5e93\uff1b\u7136\u540e\uff0c\u4f7f\u7528orthomclInstallSchema\u547d\u4ee4\u5728\u6570\u636e\u5e93\u4e2d\u521b\u5efa\u4e00\u4e9b\u8868\uff0c\u8fd9\u4e9b\u8868\u7684\u540d\u5b57\u5219\u662forthomcl.config.template\u914d\u7f6e\u6587\u4ef6\u4e2d\u6307\u5b9a\u76845\u4e2a\u540d\u79f0\u3002<\/p>\n
\r\n$ mysql -u test -p\r\nmysql> create database orthomcl;\r\n$ cp \/opt\/biosoft\/orthomclSoftware-v2.0.9\/doc\/OrthoMCLEngine\/Main\/orthomcl.config.template .\r\n$ orthomclInstallSchema orthomcl.config.template [log species]\r\n<\/pre>\n
orthomclInstallSchema\u547d\u4ee4\u540e\u9762\u4e0d\u63a5\u53c2\u6570\u5219\u7ed9\u51fa\u5e2e\u52a9\u6587\u6863\u3002\u4ee5\u4e0a\u547d\u4ee4\u4f7f\u7528orthomcl.config.template\u914d\u7f6e\u6587\u4ef6\u4e2d\u7684\u8bbe\u7f6e\u751f\u6210\u4e86\u6570\u636e\u5e93\u4e2d\u76f8\u5e94\u7684\u8868\uff0c\u5982\u679c\u52a0\u5165\u65b9\u62ec\u53f7\u4e2d\u7684\u5185\u5bb9\uff0c\u5219\u4f1a\u751f\u6210\u65e5\u5fd7\u6587\u4ef6log\uff0c\u751f\u6210\u7684\u8868\u540e\u7f00\u90fd\u662fspecies\u3002<\/p>\n
5. \u521b\u5efaorthomcl\u7684\u8f93\u5165\u6587\u4ef6<\/h1>\n
orthomcl\u7684\u8f93\u5165\u6587\u4ef6\u4e3afasta\u683c\u5f0f\u6587\u4ef6\uff0c\u4f46\u662ffasta\u6587\u4ef6\u7684\u5e8f\u5217\u540d\u79f0\u8981\u6ee1\u8db3\u8fd9\u6837\u7684\u8981\u6c42\uff1a<\/p>\n
\r\n>taxoncode|unique_protein_id\r\nMHDR...\r\n>hsa|sequence_1\r\nMHDR...\r\n>led|scaffold_1.1\r\nMHDR...\r\n<\/pre>\n
\u5e8f\u5217\u540d\u7b2c\u4e00\u5217\u662f\u7269\u79cd\u7684\u4ee3\u7801\uff0c\u4e00\u822c\u662f3\u52304\u4e2a\u5b57\u6bcd\uff1b\u4e2d\u95f4\u4f7f\u7528’|’\u7b26\u53f7\u9694\u5f00\uff1b\u7b2c\u4e8c\u5217\u662f\u86cb\u767d\u8d28\u5e8f\u5217\u72ec\u4e00\u65e0\u4e8c\u7684id\u3002
\n\u4e00\u822c\u8f93\u5165\u6587\u4ef6\u662ffasta\u683c\u5f0f\uff0c\u5176\u5e8f\u5217\u540d\u7531\u7a7a\u683c\u6216’|’\u9694\u5f00\uff0c\u4f7f\u7528orthomclAdjustFasta\u7a0b\u5e8f\uff0c\u5c06fasta\u6587\u4ef6\u8f6c\u6362\u51fa\u517c\u5bb9orthomcl\u7684fasta\u6587\u4ef6<\/p>\n
\r\n$ redun_remove protein.fasta > non_dun_protein.fasta\r\n$ mkdir compliantFasta; cd compliantFasta\r\n$ orthomclAdjustFasta led ..\/non_dun_protein.fasta 1\r\n<\/pre>\n
\u4e0a\u8ff0\u547d\u4ee4\u53bb\u9664\u53ef\u53d8\u526a\u5207\u7684\u86cb\u767d\u8d28\u5e8f\u5217\uff1b\u521b\u5efa\u4e86\u6587\u4ef6\u5939compliantFasta\uff1b\u7136\u540e\u4f7f\u7528orthomclAdjustFasta\u547d\u4ee4\u9009\u53d6\u4e86protein.fasta\u5e8f\u5217\u540d\u7684\u7b2c\u4e00\u5217\u4f5c\u4e3a\u8f93\u51fa\u7684fasta\u6587\u4ef6\u7684\u5e8f\u5217id;\u8f93\u51fa\u7684\u6587\u4ef6\u4e3aled.fasta.<\/p>\n
6. \u8fc7\u6ee4\u5e8f\u5217<\/h1>\n
\u5bf9compliantFasta\u6587\u4ef6\u5939\u4e2d\u7684\u5e8f\u5217\u8fdb\u884c\u8fc7\u6ee4\uff0c\u5141\u8bb8\u7684\u6700\u77ed\u7684protein\u957f\u5ea6\u662f10\uff0cstop codons\u6700\u5927\u6bd4\u4f8b\u4e3a20%\uff1b\u751f\u6210\u4e86\u4e24\u4e2a\u6587\u4ef6goodProteins.fasta\u548cpoorProteins.fasta\u4e24\u4e2a\u6587\u4ef6\u3002<\/p>\n
\r\n$ orthomclFilterFasta compliantFasta\/ 10 20\r\n<\/pre>\n
compliantFasta\u53ea\u80fd\u8fc7\u6ee4\u4f4e\u8d28\u91cf\u7684\u5e8f\u5217\u3002\u800c\u5b9e\u9645\u4e0a\u6700\u597d\u8fd8\u9700\u8981\u8fc7\u6ee4\u6389\u53ef\u53d8\u526a\u5207\uff0c\u53ea\u7559\u53d6\u53ef\u53d8\u526a\u5207\u4e2d\u6700\u957f\u7684\u86cb\u767d\u8d28\u5e8f\u5217\uff0c\u8fd9\u4e2a\u9700\u8981\u81ea\u884c\u89e3\u51b3\u3002<\/p>\n
7. \u5bf9goodProteins.fasta\u4e2d\u7684\u5e8f\u5217\u8fdb\u884cBLAST<\/h1>\n
\u4e0b\u8f7d\u6700\u65b0\u7248\u672c\u7684Blast+\uff0c\u548c\u6700\u65b0\u7248\u672c\u7684OrthoMCL DB\u7684protein\u5e8f\u5217<\/a>\uff0c\u5c06OrthoMCL DB\u7684protein\u5e8f\u5217\u52a0\u4e0agooProtein.fasta\u4e2d\u7684\u5e8f\u5217\u5408\u5230\u4e00\u8d77\u505a\u6210\u4e00\u4e2ablast+\u7684\u6570\u636e\u5e93\u3002\u7136\u540e\u5bf9\u57fa\u56e0\u7ec4\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\u3002<\/p>\n
\r\n$ \/opt\/biosoft\/ncbi-blast-2.2.28+\/bin\/makeblastdb -in orthomcl.fasta -dbtype prot -title orthomcl -parse_seqids -out orthomcl -logfile orthomcl.log\r\n$ \/opt\/biosoft\/ncbi-blast-2.2.28+\/bin\/blastp -db orthomcl -query goodProteins.fasta -seg yes -out orthomcl.blastout -evalue 1e-5 -outfmt 7 -num_threads 24\r\n<\/pre>\n
\u751f\u6210orthomcl\u7684blast DB\u9700\u898197\u79d2\u5de6\u53f3\uff1b\u4f7f\u7528-outfmt 7\u751f\u6210\u5e26\u6ce8\u91ca\u7684\u8868\u683c\u7ed3\u679c\uff0c\u8fd9\u4e00\u6b65\u9700\u8981\u5f88\u957f\u65f6\u95f4\u4e86\uff0c\u53d6\u51b3\u4e8e\u7535\u8111\u7684\u8fd0\u7b97\u6027\u80fd\u3002\u6211\u4f7f\u752824\u4e2a\u7ebf\u7a0b\uff0c\u6bcf\u5206\u949f\u8fd0\u884c\u7ea627.75\u6761\u5e8f\u5217\uff0c\u5927\u7ea67.2\u4e2a\u5c0f\u65f6\uff0c\u8fd0\u884c1.2\u4e07\u6761protein\u5e8f\u5217\u7684\u6bd4\u5bf9\u3002
\nblast\u4e2d\u4f7f\u7528\u4e86-seg yes\u8868\u793a\u4f7f\u7528seg\u7a0b\u5e8f\u6765\u8fdb\u884c\u8fc7\u6ee4\uff0c\u5c06\u90a3\u4e9b\u5f71\u54cd\u6bd4\u5bf9\u7ed3\u679c\u7684\u4f4e\u590d\u6742\u5ea6\u533a\u57df\u8fc7\u6ee4\u6389\u3002blast\u751f\u6210\u7684\u6587\u4ef6\u7ed3\u679c\uff0c\u4ece\u7b2c1\u5217\u5230\u7b2c12\u5217\u5206\u522b\u662f\uff1aquery id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start,  q. end,  evalue, bit score\u3002<\/p>\n
8. \u5904\u7406Blast\u7684\u7ed3\u679c<\/h1>\n
\u5bf9\u4e0a\u4e00\u6b65blast\u7684\u7ed3\u679c\u8fdb\u884c\u5904\u7406\uff0c\u4ece\u800c\u5f97\u5230\u5e8f\u5217\u7684\u76f8\u4f3c\u6027\u7ed3\u679c\uff0c\u4ee5\u7528\u4e8e\u5bfc\u5165\u5230orthomcl\u6570\u636e\u5e93\u4e2d\u3002compliantFasta\u6587\u4ef6\u5939\u4e2d\u5305\u542b\u4e0b\u8f7d\u4e0b\u6765\u7684OrthoMCL DB\u7684\u6240\u6709\u86cb\u767d\u8d28\u6570\u636e\u7684\u6587\u4ef6orthomcl.fasta.<\/p>\n
\r\n$ grep -P \"^[^#]\" orthomcl.blastout > blastresult\r\n$ orthomclBlastParser blastresult compliantFasta > similarSequences.txt\r\n$ perl -p -i -e 's\/\\t(\\w+)(\\|.*)orthomcl\/\\t$1$2$1\/' similarSequences.txt\r\n$ perl -p -i -e 's\/0\\t0\/1\\t-181\/' similarSequences.txt\r\n<\/pre>\n
\u7b2c\u4e00\u6761\u547d\u4ee4\u5c06orthomcl.blastout\u4e2d\u7684\u6ce8\u91ca\u884c\u53bb\u6389\uff0c\u751f\u6210\u65b0\u7684\u6587\u4ef6blastresult\uff0c\u4e0d\u7136\u518d\u4e0b\u4e00\u4e2a\u547d\u4ee4\u4e2d\u4f1a\u62a5\u9519\u7684\u3002
\n\u7b2c\u4e8c\u6761\u547d\u4ee4\u751f\u6210\u6587\u4ef6similarSequences.txt\uff0c\u4ece\u7b2c1\u5217\u5230\u7b2c8\u5217\u5206\u522b\u662f\uff1aquery_id, subject_id, query_taxon, subject_taxon, evalue_mant, evalue_exp, percent_ident, percent_match\u3002\u503c\u5f97\u6ce8\u610f\u7684\u662fsubject_taxon\u662forthomclBlastParser\u8bfb\u53d6\u7684\u5728compliantFasta\u6587\u4ef6\u5939\u4e2dfasta\u6587\u4ef6\u7684\u524d\u7f00\uff0c\u5728\u6b64\u7ed3\u679c\u4e2d\uff0c\u8fd9\u4e00\u5217\u5219\u5168\u662forthomcl\u3002
\n\u7b2c\u4e09\u6761\u547d\u4ee4\u5c06subject_taxon\u4fee\u6539\u4e3a\u6b63\u786e\u7684\u5206\u7c7b\u540d\u3002
\n\u7b2c\u56db\u6761\u547d\u4ee4\u4fee\u6539evalue_mant, evalue_exp,\u5c06evalue\u4e3a0\u4fee\u6539\u4e3a1e-181\uff0c\u8fd9\u5728\u540e\u7eed\u6b65\u9aa4\u5bfb\u627epairwise relationships\u65f6\u5019\u6709\u8981\u6c42\u3002<\/p>\n
9. \u5c06similarSequences.txt\u8f7d\u5165\u5230\u6570\u636e\u5e93\u4e2d<\/h1>\n
\u751f\u6210\u7684similarSequences.txt\u6587\u4ef6\u5927\u5c0f\u4e3a83M\uff0c\u5219\u4fee\u6539\/etc\/my.cnf\u6587\u4ef6\uff0c\u5728myisam_sort_buffer_size\u8fd9\u4e00\u884c\u4e0a\u52a0\u4e00\u884c\u2018myisam_max_sort_file_size = 424960\u2019\u3002\u6570\u503c\u662f83M\u76845\u500d\u3002\u7136\u540e\u8fd0\u884c\uff1a<\/p>\n
\r\n$ orthomclLoadBlast orthomcl.config.template similarSequences.txt\r\n<\/pre>\n
10. \u5bfb\u627e\u6210\u5bf9\u7684\u86cb\u767d\u8d28<\/h1>\n
\r\n$ orthomclPairs orthomcl.config.template orthomcl_pairs.log cleanup=no\r\n<\/pre>\n
\u8f93\u5165\u4e3a\u6570\u636e\u5e93\u4e2d\u7684\u8868SimilarSequences\uff0c\u548c\u6570\u636e\u5e93\u7684\u7a7a\u8868InParalog, Ortholog, CoOrtholog tables\uff1b\u8f93\u51fa\u4e3a\u5bf9\u8fd9\u4e9b\u7a7a\u8868\u7684\u64cd\u4f5c\u3002\u6545\u914d\u7f6e\u6587\u4ef6\u4e2d\u7684\u7528\u6237\u8981\u6709 update\/insert\/truncate\u6743\u9650\u3002<\/p>\n
11. \u5c06\u6570\u636e\u4ece\u6570\u636e\u5e93\u4e2d\u5bfc\u51fa<\/h1>\n
\r\n$ orthomclDumpPairsFiles orthomcl.config.template\r\n<\/pre>\n
\u751f\u6210\u4e86\u4e00\u4e2a\u6587\u4ef6mclInput\u548c\u4e00\u4e2a\u6587\u4ef6\u5939pairs\uff1b\u6587\u4ef6\u5939\u4e2d\u5305\u542b3\u4e2a\u6587\u4ef6coorthologs.txt\uff0cinparalogs.txt\uff0corthologs.txt\u3002<\/p>\n
12. \u4f7f\u7528mcl\u8fdb\u884c\u5bf9pairs\u8fdb\u884c\u805a\u7c7b<\/h1>\n
\r\n$ mcl mclInput --abc -I 1.5 -o mclOutput\r\n<\/pre>\n
13. \u5bf9mcl\u7684\u805a\u7c7b\u7ed3\u679c\u8fdb\u884c\u7f16\u53f7<\/h1>\n
\r\n$ orthomclMclToGroups led 1 < mclOutput > groups.txt\r\n<\/pre>\n
\u5bf9\u805a\u7c7b\u7ed3\u679c\u8fdb\u884c\u7f16\u53f7\uff0c\u4f9d\u6b21\u4e3aled1\uff0cled2, led3…<\/p>\n
\u6ce8\u610f\u4e8b\u9879<\/h1>\n
\u7b2c7\u6b65Blast\uff0c\u662f\u6574\u4e2a\u8fc7\u7a0b\u4e2d\u6700\u5173\u952e\u7684\u4e00\u6b65\u3002\u6709\u4ee5\u4e0b2\u70b9\u9700\u8981\u6ce8\u610f\uff1a
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