Ken Youens-Clark > Bio-SSRTool > Bio::SSRTool

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NAME ^

Bio::SSRTool - The great new Bio::SSRTool!

SYNOPSIS ^

Examines FASTA-formatted sequence data for simple sequence repeats (SSRs).

    use Bio::SSRTool;

EXPORT ^

SUBROUTINES/METHODS ^

find_ssr

    my $ssr_tool = Bio::SSRTool->new();
    my @ssrs = $ssr_tool->find_ssr( $seq, { min_repeats => 10 } );

Or:

    use Bio::SSRTool 'find_ssr';

    my @ssrs = find_ssr( $fh, { motif_length => 'trimer' } );

The "find_ssr" routine expects a sequence string in FASTA format (or a filehandle to read a FASTA file) and an optional hash-ref of arguments including:

min_repeats

A positive integer

motif_length

A positive integer between 1 and 10. Default is 4.

AUTHOR ^

Ken Youens-Clark, <kclark at cpan.org>

BUGS ^

Please report any bugs or feature requests to bug-bio-ssrtool at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-SSRTool. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT ^

You can find documentation for this module with the perldoc command.

    perldoc Bio::SSRTool

ACKNOWLEDGEMENTS ^

This was originally written in 1999 by Sam Cartinhour. Thanks to Jim Thomason for code review.

LICENSE AND COPYRIGHT ^

Copyright 2012 Ken Youens-Clark.

This program is released under the following license: GPL

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