NAME
Bio::DOOP::Motif - DOOP database motif object
VERSION
Version 0.7
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 an evolutionary conserved motif from a subset.
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
new
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");
type
Returns the type of the motif.
Return type : string
$motif_type = $motif->type;
seq
Returns the consensus sequence of the motif.
Return type: string
$motif_seq = $motif->seq;
start
Returns the start position of the motif.
Return type: string
$start = $motif->start;
end
Returns the end position of the motif.
Return type: string;
$end = $motif->end;
length
Returns the length of the motif.
Return type: string
$length = $motif->length;
get_id
Returns the primary ID of the motif. This is the internal ID from the MySQL database.
Return type: string
$primary_id = $motif->get_id;
get_subset_id
Returns the motif subset primary id.
Return type: string
$subset_id = $motif->get_subset_id;
get_seqfeats
Returns all the sequence features, associated with the motif. This basically means all the sequence regions from which the motif was generated.
Return type: arrayref, the array containing Bio::DOOP::SequenceFeature objects.
@feats = @{$motif->get_seqfeats}