[Bioperl-l] Getting IC & Consensus with Bio::Matrix::PSM::SiteMatrix

Edward Wijaya ewijaya at singnet.com.sg
Sun Mar 13 22:04:40 EST 2005


Why my code below fails to return the IC values?
I thought the method is able to do that.
Is there anything I miss here?

My second question is about"consensus" method.
The consensus is generated by choosing the highest probability OR *N if  
prob is too low*

1. How do you define when the probability is *too low*?
2. What is the reasoning behind this implementation?
    e.g. Why my code below gives 'TANGTA' instead of "TATGTA"?

I find this particular module is very very useful.
I really wish I can make best use of it.

Thanks so much for your time.
Hope to hear from you again.



#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Bio::Matrix::PSM::SiteMatrix;

      #Frequency matrix
      my  @pA = (2,19,3,6,8,10);
      my  @pT = (7,3,6,2,20,5);
      my  @pC = (1,2,2,1,1,1);
      my  @pG = (3,1,1,9,8,7);

my %param =( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT);
my $site=new Bio::Matrix::PSM::SiteMatrix(%param);

my $consensus = $site->consensus;
my $ic = $site->IC; #Why it fails here?

print Dumper $ic;
print Dumper $consensus;


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