NAME

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

VERSION

Version 1.02

SYNOPSIS

use Bio::DOOP::DOOP;

# to connect to the primary database uncomment the following lines
# $user = "promoter";
# $pass = "sql04CP";
# $database = "doop-chordate-1_4"; # for vertebratas
# $database = "doop-plant-1_6"; # for plants
# $host = "bioweb.abc.hu";

$db = Bio::DOOP::DBSQL->connect($user,$pass,$database,$host);
$cluster = Bio::DOOP::Cluster->new($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 or read the following article.

Endre Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, and László Patthy
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream 
sequences from chordates and plants
Nucl. Acids Res. 2005, Vol 33, Database issue D86-D90

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.

If you would like to connect to the database of Agricultural Biotechnology Center,
you can use the following syntax:

Bio::DOOP::DBSQL->connect("promoter", "sql04CP", "doop-choordate-1_4", "bioweb.abc.hu");

AUTHORS

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

OBJECTS

Bio::DOOP::DBSQL

Object for simple SQL queries. Use it to connect to the database.
This is the first module you should use.

Bio::DOOP::Cluster

Object for the clusters. Cluster is a homologue promoter collection.

Bio::DOOP::ClusterSubset

Object for the subsets of sequences in a cluster.

Bio::DOOP::Sequence

Object for the sequences.

Bio::DOOP::SequenceFeature

Object for the different features of a sequence.

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

MOFEXT wrapper. MOFEXT is a motif search 
tool developed by the author Tibor Nagy.

Bio::DOOP::Util::Run::Fuzznuc

FUZZNUC wrapper. Install Emboss to use this.

Bio::DOOP::Util::Run::GeneMerge

GeneOntology analyzer, based on the program
GeneMerge.

Bio::DOOP::Util::Run::Admin

Module for controlling the Mofext, Fuzznuc wrapper processes.

Bio::DOOP::Graphics::Feature

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

COPYRIGHT & LICENSE

Copyright 2009 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.

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP