OrthoMCL 使用笔记

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BLAST

配置 MCL 的 MySQL 数据库

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$ create database orthomcl;
$ DROP TABLE BestHit, BestInterTaxonScore, BestQueryTaxonScore, BetterHit, CoOrthNotOrtholog, CoOrtholog, CoOrthologAvgScore, CoOrthologCandidate, CoOrthologTaxon, CoOrthologTemp, InParalog, InParalog2Way, InParalogAvgScore, InParalogOrtholog, InParalogTaxonAvg, InParalogTemp, InplgOrthTaxonAvg, InplgOrthoInplg, InterTaxonMatch, Ortholog, Ortholog2Way, OrthologAvgScore, OrthologTaxon, OrthologTemp, OrthologUniqueId, SimilarSequences, UniqSimSeqsQueryId;
$ DROP TABLE BestQueryTaxonScore;
$ orthomclInstallSchema orthomcl.config.template

载入数据到 MySQL

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$ orthomclLoadBlast orthomcl.config.template similarSequences.txt
$ orthomclLoadBlast orthomcl.config.template similarSequences.txt.rmisoform
$ orthomclPairs orthomcl.config.template orthomcl_pairs.log cleanup=no
$ orthomclDumpPairsFiles orthomcl.config.template

运行 OrthoMCL

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$ mcl mclInput --abc -I 1.1 -o mclOutput11
$ orthomclMclToGroups ORYSA 1 < mclOutput11 > groups11x.txt

结果文件的使用

Reference