[Bioperl-l] repeatmasker

Chris Fields cjfields at uiuc.edu
Tue Jan 2 11:21:26 EST 2007


RepeastMasker.pm is a wrapper for the RepeatMasker program.  This is  
from the POD:

DESCRIPTION
        RepeatMasker is a program that screens DNA sequences for  
interspersed
        repeats known to exist in mammalian genomes as well as for  
low complex-
        ity DNA sequences. For more information, on the program and  
its usage,
        please refer to http://repeatmasker.genome.washington.edu/.

Newer versions are available here:

http://www.repeatmasker.org/

You need to install RepeatMasker in your PATH in order to use the  
wrapper.

chris

On Jan 2, 2007, at 8:59 AM, Karen Buysse wrote:

> Dear all,
>
> I want to use the BioPerl repeatmasker program.
> However, when I run the following program (=first lines of the  
> synopsis):
>
> use Bio::Tools::Run::RepeatMasker;
>
>   my @params=("mam" => 1,"noint"=>1);
>   my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
>
> I get the error message: *RepeatMasker program not found as  or not
> executable.*
> I have the file *RepeatMasker.pm* in the following directories:
> C:/Perl/lib/Bio/Tools/Run
> C:/Perl/site/lib/Bio/Tools/Run
>
> Can anyone please help me with this?
>
> Many thanks in advance and a happy new year,
> Karen
>
> -- 
> ir. Karen Buysse
> Center for Medical Genetics Ghent (CMGG)
> Ghent University Hospital
> Medical Research Building (MRB), 2nd floor, room 120.050
> De Pintelaan 185, B-9000 Ghent, Belgium
> +32 9 240 39 46 (phone)
> +32 9 240 65 49 (fax)
> http://medgen.ugent.be
> Karen.Buysse at UGent.be
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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