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>
<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.
bug-Seeder at rt.cpan.org
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.
1 POD Error
The following errors were encountered while parsing the POD:
Non-ASCII character seen before =encoding in 'François'. Assuming UTF-8
To install Seeder, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Seeder
CPAN shell
perl -MCPAN -e shell install Seeder
For more information on module installation, please visit the detailed CPAN module installation guide.