Bio::DOOP::Motif - DOOP database motif object
Version 0.7
use Bio::DOOP::Motif; $db = Bio::DOOP::DBSQL->connect("user","pass","database","somewhere.where.org"); my $motif = Bio::DOOP::Motif->new($db,"160945"); print $motif->seq,":",$motif->start," ",$motif->end,"\n";
This object represents an evolutionary conserved motif from a subset.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
Creates a new motif object from the motif primary id. You usually won't need this, as you will get this object from other objects.
Return type: Bio::DOOP::Motif object.
$motif = Bio::DOOP::Motif->new($db,"1234");
Returns the type of the motif.
Return type : string
$motif_type = $motif->type;
Returns the consensus sequence of the motif.
Return type: string
$motif_seq = $motif->seq;
Returns the start position of the motif.
$start = $motif->start;
Returns the end position of the motif.
Return type: string;
$end = $motif->end;
Returns the length of the motif.
$length = $motif->length;
Returns the primary ID of the motif. This is the internal ID from the MySQL database.
$primary_id = $motif->get_id;
Returns the motif subset primary id.
$subset_id = $motif->get_subset_id;
Returns all the sequence features, associated with the motif. This basically means all the sequence regions from which the motif was generated.
Return type: arrayref, the array containing Bio::DOOP::SequenceFeature objects.
@feats = @{$motif->get_seqfeats}
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.