Bio::DOOP::DOOP - DOOP API main module
Version 0.24
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"; }
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.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
Object for simple SQL queries.
Object for the clusters.
Object for the subsets of sequences inside a cluster.
Object for the cluster (or cluster subset) sequences.
Object for the different features of the sequences.
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.
Module for Mofext wrapping. Mofext is a motif finder program developed by the author Tibor Nagy.
Module for controll Emboss program fuzznuc.
Module for controll all the running DOOP wrapper objects
Module for generating a picture of the sequences and feature of a cluster.
Copyright 2006 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.