NAME

  Bio::DOOP::Util::Search - useful subrutines for easy search

VERSION

Version 0.01

SYNOPSIS

  use Bio::DOOP::DOOP;

  $db = Bio::DOOP::DBSQL->connect("doopuser","dooppasswd","doop-plant","localhost");
  @motifs = @{Bio::DOOP::Util::Search::get_all_motifs_by_type($db,"V")};

DESCRIPTION

  Collection of utilities managing big queries. Most of
  the subrutines return arrayrefs of motifs, sequences, clusters.
  For example: You want all the motifs that can be found in al of the
  subsets. Instead of you go through all the motif in the jungle of 
  SQL querys, you use the ... subrutine. Your code will be more 
  simple.

AUTHOR

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

SUBRUTINES

get_all_motifs_by_type

  Return the arrayref of all motifs that type is specified in the argument.

get_all_original_subset

  Return the arrayref of all original subset.

get_all_cluster_by_gene_id

  Return the arrayref of all clusters defined by the gene id

get_all_cluster_by_keyword

  Return all clusters that is contain the keyword in its description, tss annotation or sequence xref

get_all_cluster_by_type

  Return the arrayref of clusters that xref contain this type and value

get_all_cluster_by_taxon_name

  Return the arrayref of clusters that is contain this taxon name

get_all_cluster_by_taxon_id

  Return the arrayref of clusters that is contain this taxon id

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

  Return the arrayref of sequences containing the given motif id

cpanm Bio::DOOP::DOOP

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