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Bio::Tools::Run::TribeMCL 1.4

  Date Added: March 27, 2010  |  Visits: 1.115

Bio::Tools::Run::TribeMCL

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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 = [[qw(ENSP00000257547 ENSP00000261659 1 50)], [qw(O42187 ENSP00000257547 1 119)]]; 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 = [ [mem1 mem2 mem3],[mem1 mem2 mem3]] # 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.

Requirements: No special requirements
Platforms: Linux
Keyword: Biotoolsruntribemcl Clustering Groups Libraries Params Programming Protein Proteins Related Tribemcl
Users rating: 0/10

License: Freeware Size: 829.44 KB
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