Bio::DOOP::Util::Search - Useful methods for easy search

Version 0.13

  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")};

Collection of utilities handling large queries. Most of the methods return arrayrefs of motifs, sequences or clusters.

Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

Returns the arrayref of motifs with the type specified in the arguments.

Returns the arrayref of all original subsets.

Returns the arrayref of all Bio::DOOP::Cluster objects, defined by a gene id.

Returns the arrayref of all Bio::DOOP::Cluster objects, containing the keyword in their description or tss annotation.

Returns the arrayref of Bio::DOOP::Clsuter objects, containing a given xref.

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!

Returns the arrayref of cluster ids containing the taxon name. Don't use this, use get_all_cluster_by_taxon_id with NCBI IDs!

Returns the arrayref of Bio::DOOP::Cluster objects, containing an NCBI taxon id.

Returns the arrayref of cluster ids containing an NCBI taxon id.

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given sequence id (fake GI).

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given At Number.

Returns the arrayref of Bio::DOOP::Sequence objects, containing a given motif id.

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given GO ID.

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given ENSEMBL gene 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.