Bio::DOOP::DOOP - DOOP API main module
Version 1.04
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");
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");
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
Object for simple SQL queries. Use this to connect to the database. This is the first module you should use.
Object for the clusters. A cluster is a homologous promoter collection.
Object for different subsets of sequences in a given cluster.
Object for a sequences of a cluster.
Object for the different features of a sequence.
Object for the conserved sequence features.
Module for different search subrutines.
Sort an array of array by given conditions.
Filter a cluster array by given conditions.
MOFEXT wrapper. MOFEXT is a motif search tool developed by Tibor Nagy.
FUZZNUC wrapper. Install EMBOSS to use this.
GeneOntology analyzer, based on the program GeneMerge.
Module for generating a PNG picture of the sequences and features of a cluster.
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.
To install Bio::DOOP::DOOP, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DOOP::DOOP
CPAN shell
perl -MCPAN -e shell install Bio::DOOP::DOOP
For more information on module installation, please visit the detailed CPAN module installation guide.