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