NAME

  Bio::DOOP::Util::Search - useful methods for easy search.

VERSION

  Version 0.12

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 clusters defined by the gene id.

get_all_cluster_by_keyword

  Returns the arrayref of all clusters containing the keyword in their description or tss annotation.

get_all_cluster_by_xref

  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 cluster ids 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

  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.

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP