[Bioperl-l] automated stand alone blast with repeat masker

vdar at yorku.ca vdar at yorku.ca
Tue May 13 16:56:18 EDT 2008

Following is the path to repeatmasker.pm on my system


but when I run my program, the error message comes

RepeatMasker program not found as  or not executable

Here is my piece of code which gives this error,

use strict;
use warnings;

use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
use Bio::Search::Hit::HitI;
use Bio::Search::Hit::BlastHit;
use Bio::Search::HSP::BlastHSP;
use Bio::Search::HSP::HSPI;
use Bio::SearchIO;
use Bio::Tools::Run::RepeatMasker;


	$ENV{REPEATMASKERDIR} = '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/';


my @params = ("mam" => 1,"noint"=>1);
my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
my $in  = Bio::SeqIO->new(-file => "boechera.fasta", -format => 'fasta');

I tried finding RepeatMasker directory by typing

which RepeatMasker

but the error message was

/usr/bin/which: no RepeatMasker in

Quoting Dave Messina <David.Messina at sbc.su.se>:

> I haven't done this myself, but from a quick search on the BioPerl website,
> it looks like you'll want to use the
> to create a repeat-masked fasta file.
> If you RepeatMask your query sequence(s), then you need to specify that
> sequence when you create your Bio::Seq object.
> If you instead RepeatMask your database, you'll need to create a blast
> database from the repeat-masked sequences and specify that db in your
> @params. I don't think there's a module for running formatdb, but you can do
> it through a system call.
> Dave

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