NAME
Bio::DOOP::Util::Search - useful methods for easy search.
VERSION
Version 0.11
SYNOPSIS
use Bio::DOOP::DOOP;
$db = Bio::DOOP::DBSQL->connect("doopuser","dooppasswd","database","localhost");
@motifs = @{Bio::DOOP::Util::Search::get_all_motifs_by_type($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
SUBRUTINES
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 clusters defined by the gene id.
get_all_cluster_by_keyword
Returns all clusters containing the keyword in its description, tss annotation or sequence xref.
get_all_cluster_by_type
Returns the arrayref of clusters containing a given xref.
get_all_cluster_by_taxon_name
Returns the arrayref of clusters containing the 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 clusters containing the taxon id (NCBI).
get_all_cluster_id_by_taxon_id
Returns the arrayref of clusters id containing the taxon id (NCBI).
get_all_cluster_by_sequence_id
Returns the arrayref of clusters containing the given sequence id (fake GI).
get_all_cluster_by_atno
Returns the arrayref of clusters containing the given At Number.
get_all_seq_by_motifid
Returns the arrayref of sequences containing the given motif id.
get_all_cluster_by_go_id
20070221 E. Sebestyen
Returns the arrayref of clusters containing the given GO ID.
get_all_cluster_by_ensno
Returns the arrayref of clusters containing the 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.
E. Sebestyen 20070518