[Bioperl-l] Bio::SearchDist problem

Gabor Toth tothg at abc.hu
Sat Sep 10 09:22:19 EDT 2005


I would like to use Bio::SearchDist to fit an extreme value distribution to a 
sorted set of 20724 integer scores and calculate E-value for each score. The 
scores are distributed around a median of zero with a range between -204 and 

However, using the script below, I cannot get meaningful E-values. The first 
29 "E-values" are 1075530112, the 30th is 1, and all other are zero.
(The input and output files can be found here: 
My BioPerl version is 1.4.

What am I doing wrong?
I will appreciate any help,

Gabor Toth

#!/usr/bin/perl -w

use Bio::SearchDist;

$dis = Bio::SearchDist->new();

while (<>) {
    push @scores, $_;

if ( $dis->fit_evd() ) {
    foreach $score (@scores) {
	$evalue = $dis->evalue($score);
	print "S: $score   E: $evalue\n";
else {
    warn("Cannot fit!");

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