Seeder 0.01

Seeder is a Perl module, a base class and is not meant to be instantiated itself.

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 (believe to contain a similar cis-regulatory element) and a background set of DNA sequences in fasta format.

To discover motifs in DNA sequences, follow this sequence:

(1) Generation of the index (this structure improves the performance of HD calculation). Restrict seed width to between 6 and 8.

 use Seeder::Index;
 my $index = Seeder::Index->new(
 seed_width => "6",
 out_file => "6.index",
 );
 $index->get_index;

(2) Generation of the background distributions.

 use Seeder::Background;
 my $background = Seeder::Background->new(
 seed_width => "6",
 strand => "revcom",
 hd_index_file => "6.index",
 seq_file => "seqs.fasta",
 out_file => "seqs.bkgd",
 );
 $background->get_background;

(3) Motif discovery.

 use Seeder::Finder;
 my $finder = Seeder::Finder->new(
 seed_width => "6",
 strand => "revcom",
 motif_width => "12",
 n_motif => "1",
 hd_index_file => "6.index",
 seq_file => "prom.fasta",
 bkgd_file => "seqs.bkgd",
 out_file => "prom.finder",
 );
 $finder->find_motifs;


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Requirements:

· Perl