Bio::DOOP::Util::Search - useful methods for easy search.
Version 0.12
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 clusters defined by the gene id.
Returns the arrayref of all clusters containing the keyword in their description or tss annotation.
Returns the arrayref of clusters containing a given xref.
Returns the arrayref of clusters containing the 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 clusters containing the taxon id (NCBI).
Returns the arrayref of cluster ids containing the taxon id (NCBI).
Returns the arrayref of clusters containing the given sequence id (fake GI).
Returns the arrayref of clusters containing the given At Number.
Returns the arrayref of sequences containing the given motif id.
Returns the arrayref of clusters containing the given GO ID.
Returns the arrayref of clusters containing the 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.
To install Bio::DOOP::DOOP, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DOOP::DOOP
CPAN shell
perl -MCPAN -e shell install Bio::DOOP::DOOP
For more information on module installation, please visit the detailed CPAN module installation guide.