Seeder - Motif discovery in DNA sequences

Version 0.01

This module is 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;

None by default

 Title   : read_hd_index
 Usage   : $self->read_hd_index;
 Function: read the index file
 Returns : reference to a 2D array of positive integers
 Args    : none

 Title   : generate_oligo
 Usage   : $self->generate_oligo;
 Function: generate all combinations of nucleotides for a given word length,
           represented by numbers (0=>A, 1=>C, 2=>G, 3=>T)
 Returns : reference to a 2D array of oligos
 Args    : none

 Title   : lookup_coord
 Usage   : $self->lookup_coord;
 Function: generate indices for lookup (HD calculation)
 Returns : reference to 2D arrays of begin/end lookup indices
 Args    : none

 Title   : bc_factor
 Usage   : my $bc_factor_ref = $self->bc_factor;
 Function: generate the number of neighbors in function of Hamming distance
           and seed width
 Returns : references to a 2D array of number of neighbors
 Args    : none

 Title   : _factorial
 Usage   : my $r = _factorial($n);
 Function: calculate the product of all positive integers less than or equal
           to a given number
 Returns : non-negative integer
 Args    : none

 Title   : generate_hd_index
 Usage   : my $hd_index = $self->generate_hd_index( $oligo_ref );
 Function: generate oligo indices for increasing Hamming distances
 Returns : array of indices
 Args    : reference to oligo

 Title   : execution_time
 Usage   : my $time_string = $self->execution_time;
 Function: transform a lapse of time in "seconds since epoch" into a
           human-readable format
 Returns : lapse of time (string) 
 Args    : none

 Title   : encode
 Usage   : my $representation = encode($value, $base, $depth);
 Function: convert value (base 10) to representation in specified base
 Returns : array or integers from 0 to 3
 Args    : base 10 number to be converted, base to which the number is
           converted, width of the representation

 Title   : decode
 Usage   : my $value = decode($representation, $base);
 Function: convert representation to value (base 10)
 Returns : integer
 Args    : representation, base of the representation

François Fauteux, <ffauteux at cpan.org>

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

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

    perldoc Seeder

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

This algorithm was developed by François Fauteux, Mathieu Blanchette and Martina Strömvik. We thank the Perl Monks <http://www.perlmonks.org/> for their support.

Copyright 2008 François Fauteux, all rights reserved.

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