Bio::Tools::Run::TribeMCL Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'.
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Perl module Clustering clustering proteins protein families proteins

Bio::Tools::Run::TribeMCL Description

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'.SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params = ('inputtype'=>'blastfile'); # OR # markov program format # protein_id1 protein_id2 evalue_magnitude evalue_factor # for example: # proteins ENSP00000257547 and ENSP00000261659 # with a blast score evalue of 1e-50 # and proteins O42187 and ENSP00000257547 # with a blast score evalue of 1e-119 # entry would be my @array = , ]; my @params = ('pairs'=>@array,I=>'2.0'); # OR # pass in a searchio object # slowest of the 3 methods as it does more rigourous parsing # than required for us here my $sio = Bio::SearchIO->new(-format=>'blast', -file=>'blast.out'); my @params=('inputtype'=>'searchio',I=>'2.0'); # you can specify the path to the executable manually in the following way my @params=('inputtype'=>'blastfile',I=>'2.0', 'mcl'=>'/home/shawn/software/mcl-02-150/src/shmcl/mcl', 'matrix'=>'/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix'); my $fact = Bio::Tools::Run::TribeMCL->new(@params); # OR $fact->matrix_executable('/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix'); $fact->mcl_executable('/home/shawn/software/mcl-02-150/src/shmcl/mcl'); # to run my $fact = Bio::Tools::Run::TribeMCL->new(@params); # Run the program # returns an array reference to clusters where members are the ids # for example :2 clusters with 3 members per cluster: # $fam = ,] # pass in either the blastfile path/searchio obj/the array ref to scores my $fam = $fact->run($sio); # print out your clusters for (my $i = 0; $i })." membersn"; foreach my $member (@{$fam->}){ print "t$membern"; } }This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases, proteins in the same protein family will have similar functional properties.What's New in This Release:· Perl

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