Seeder version 0.01
======================

  Seeder is a framework for DNA motif discovery. It is designed for efficient
  and reliable prediction of regulatory motifs in eukaryotic promoters. In
  order to generate DNA motifs, you need one positive set of DNA sequences in
  fasta format and one background set of DNA sequences in fasta format.

CONTACT INFO

  Author      : francois.fauteux2@mail.mcgill.ca
  Bug reports : contact author

SYSTEM REQUIREMENTS

  - Perl 5.6.0 or later

DEPENDENCIES

  - Carp
  - List::Util
  - List::MoreUtils
  - Algorithm::Loops
  - Math::Spline
  - Bioperl
    o Bio::SeqIO
    o Bio::LiveSeq::DNA
    o Bio::LiveSeq::SeqI

INSTALLATION

  perl Makefile.PL
  make
  make test
  make install

USAGE

  To perform motif discovery, follow this sequence of operations:

  (1) Generation of  the index with the Seeder::Index module.

  (2) Generation of the background distributions with the Seeder::Background
      module.

  (3) Motif discovery with the Seeder::Finder module.

SUPPORT AND DOCUMENTATION

  After installing, you can find documentation for this module with the
  perldoc command.

    perldoc Seeder
    perldoc Seeder::Index
    perldoc Seeder::Background
    perldoc Seeder::Finder

  You can also look for information at:

    RT, CPAN's request tracker
        http://rt.cpan.org/NoAuth/Bugs.html?Dist=Seeder

    AnnoCPAN, Annotated CPAN documentation
        http://annocpan.org/dist/Seeder

    CPAN Ratings
        http://cpanratings.perl.org/d/Seeder

    Search CPAN
        http://search.cpan.org/dist/Seeder


COPYRIGHT AND LICENCE

  Copyright (C) 2008 François Fauteux

  This program is free software; you can redistribute it and/or modify it
  under the same terms as Perl itself.