Bio::Tools::Run::TribeMCL 1.4

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
print "Cluster $i t ".scalar(@{$fam->[$i]})." membersn";
foreach my $member (@{$fam->[$i]}){
print "t$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.
Enhancements:
- Perl