Author image Endre Sebestyen
and 1 contributors

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.