/ 
Bio-DOOP-DOOP-0.1
/ Bio::DOOP::DOOP

NAME

Bio::DOOP::DOOP - DOOP API main module

VERSION

Version 0.1

SYNOPSIS

use Bio::DOOP::DOOP;

$db = Bio::DOOP::DBSQL->new("doopuser","dooppass","database","localhost");
$cluster = Bio::DOOP::Cluster->new($db,"8010109","500");
@seqs = @{$cluster->get_all_seqs};
foreach $seq (@seqs){
   print $seq->seq,"\n";
}

DESCRIPTION

DoOP is a database containing orthologous clusters of promoters from Homo sapiens, 
Arabidopsis thaliana and other organisms. Visit the http://doop.abc.hu/ site for
more information.
This is a container module for all of the DOOP modules.
You can simply use this module to access all DOOP objects.
For more help, please see the documentation of the individual
objects.

AUTHOR

Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

OBJECTS

Bio::DOOP::DBSQL

Object for simple SQL queries.

Bio::DOOP::Cluster

Object for the clusters.

Bio::DOOP::ClusterSubset

Object for the subsets of sequences inside a cluster.

Bio::DOOP::Sequence

Object for the cluster (or cluster subset) sequences.

Bio::DOOP::SequenceFeature

Object for the different features of the sequences.

Bio::DOOP::Motif

Object for the conserved sequence features.

Bio::DOOP::Util::Search

Module for different search subrutines.

Bio::DOOP::Util::Run::Mofext

Module for Mofext wrapping. Mofext is a motif finder 
program developed by the author Tibor Nagy.

Bio::DOOP::Graphics::Feature

Module for generating a picture of the sequences and feature of a cluster.

COPYRIGHT & LICENSE

Copyright 2006 Tibor Nagy, all rights reserved.

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