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.