NAME

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

VERSION

Version 1.00

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.

AUTHORS

  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

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

CPAN RT