NAME
Bio::DOOP::Motif - DOOP database motif object
VERSION
Version 0.6
SYNOPSIS
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";
DESCRIPTION
This object represents the conserved motifs.
You should not use the constructor directly, but
sometimes it can be useful. In most cases you
get this object from other objects.
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
new
$motif = Bio::DOOP::Motif->new($db,"1234");
You can create the object with the new method.
The arguments are the following : Bio::DOOP::DBSQL object, motif_primary_id
type
$motif_type = $motif->type;
Returns the type of the motif.
Return type : string
seq
$motif_seq = $motif->seq;
Returns the consensus sequence of the motif.
Return type : string
start
$start = $motif->start;
Returns the start position of the motif.
Return type : string
end
$end = $motif->end;
Returns the end position of the motif.
Return type : string;
length
$length = $motif->length;
Returns the length of the motif.
Return type : string
get_id
$primary_id = $motif->get_id;
Returns the primary ID of the motif. This is the internal ID from the MySQL database.
Return type : string
get_subset_id
$subset_id = $motif->get_subset_id;
Returns the motif subset primary id.
Return type : string
get_seqfeats
@feats = @{$motif->get_seqfeats}
Returns all the sequence features, associated with the motif.
Return type : arrayref, the array containing Bio::DOOP::SequenceFeature objects.