NAME
Bio::DOOP::DOOP - DOOP API main module
VERSION
Version 0.25
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::Sort
Sort an array of array by given conditions.
Bio::DOOP::Util::Filt
Filter a Cluster array by given conditions.
Bio::DOOP::Util::Run::Mofext
Module for Mofext wrapping. Mofext is a motif finder
program developed by the author Tibor Nagy.
Bio::DOOP::Util::Run::Fuzznuc
Module for controll Emboss program fuzznuc.
Bio::DOOP::Util::Run::Admin
Module for controll all the running DOOP wrapper objects
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.