NAME
Bio::DOOP::DOOP - DOOP API main module
VERSION
Version 1.01
SYNOPSIS
use Bio::DOOP::DOOP;
$db = Bio::DOOP::DBSQL->new("user","pass","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 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.
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 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.
Bio::DOOP::Util::Run::GeneMerge
GeneOntology analyzer, based on the program
GeneMerge.
Bio::DOOP::Util::Run::Admin
Module for controlling the different wrappers.
Bio::DOOP::Graphics::Feature
Module for generating a picture of the sequences and features of a cluster.
COPYRIGHT & LICENSE
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.
1 POD Error
The following errors were encountered while parsing the POD:
- Around line 49:
Non-ASCII character seen before =encoding in 'Sebestyén,'. Assuming UTF-8