Author image Endre Sebestyen
and 1 contributors

NAME

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

VERSION

Version 1.04

SYNOPSIS

  use Bio::DOOP::DOOP;

  # to connect to the primary database use the parameters in the
  # following example

  $user     = "promoter";
  $pass     = "sql04CP";
  $database = "doop-chordate-1_4"; # latest chordate database
  $database = "doop-plant-1_6";    # latest plant database
  $host     = "bioweb.abc.hu";

  $db = Bio::DOOP::DBSQL->connect($user,$pass,$database,$host);

  # in one line

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

DESCRIPTION

DoOP is a database containing orthologous clusters of promoters from Homo sapiens, Arabidopsis thaliana and other organisms. Visit the doop.abc.hu or doopsearch.abc.hu sites for more information or read the following article.

Endre Barta, Endre Sebestyen, Tamas B. Palfy, Gabor Toth, Csaba P. Ortutay, and Laszlo 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 a more detailed help, use the documentation of the individual objects.

If you would like to connect to the MySQL database of Agricultural Biotechnology Center (www.abc.hu), use the following syntax.

  $db = 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 this to connect to the database. This is the first module you should use.

Bio::DOOP::Cluster

Object for the clusters. A cluster is a homologous promoter collection.

Bio::DOOP::ClusterSubset

Object for different subsets of sequences in a given cluster.

Bio::DOOP::Sequence

Object for a sequences of a cluster.

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 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::Graphics::Feature

Module for generating a PNG 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.