NAME
Bio::DOOP::Util::Search - Useful methods for easy search
VERSION
Version 0.13
SYNOPSIS
use Bio::DOOP::DOOP;
$db = Bio::DOOP::DBSQL->connect("user","passwd","database","localhost");
@motifs = @{Bio::DOOP::Util::Search::get_all_motifs_by_type($db,"V")};DESCRIPTION
Collection of utilities handling large queries. Most of the methods return arrayrefs of motifs, sequences or clusters.
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
get_all_motifs_by_type
Returns the arrayref of motifs with the type specified in the arguments.
get_all_original_subset
Returns the arrayref of all original subsets.
get_all_cluster_by_gene_id
Returns the arrayref of all Bio::DOOP::Cluster objects, defined by a gene id.
get_all_cluster_by_keyword
Returns the arrayref of all Bio::DOOP::Cluster objects, containing the keyword in their description or tss annotation.
get_all_cluster_by_xref
Returns the arrayref of Bio::DOOP::Clsuter objects, containing a given xref.
get_all_cluster_by_taxon_name
Returns the arrayref of Bio::DOOP::Cluster objects containing a taxon name. Don't use this, use get_all_cluster_by_taxon_id with NCBI IDs!
get_all_cluster_id_by_taxon_name
Returns the arrayref of cluster ids containing the taxon name. Don't use this, use get_all_cluster_by_taxon_id with NCBI IDs!
get_all_cluster_by_taxon_id
Returns the arrayref of Bio::DOOP::Cluster objects, containing an NCBI taxon id.
get_all_cluster_id_by_taxon_id
Returns the arrayref of cluster ids containing an NCBI taxon id.
get_all_cluster_by_sequence_id
Returns the arrayref of Bio::DOOP::Cluster objects, containing a given sequence id (fake GI).
get_all_cluster_by_atno
Returns the arrayref of Bio::DOOP::Cluster objects, containing a given At Number.
get_all_seq_by_motifid
Returns the arrayref of Bio::DOOP::Sequence objects, containing a given motif id.
get_all_cluster_by_go_id
Returns the arrayref of Bio::DOOP::Cluster objects, containing a given GO ID.
get_all_cluster_by_ensno
Returns the arrayref of Bio::DOOP::Cluster objects, containing a given ENSEMBL gene ID.
get_all_cluster_id
Returns an arrayref of all the cluster IDs of a given promoter/subset category. For example returns all clusters with 1000 bp E type subsets.