/ 
Bio-DOOP-DOOP-0.1
River stage zero No dependents
/ Bio::DOOP::Motif

NAME

Bio::DOOP::Motif - DOOP database conserved motif object

VERSION

Version 0.08

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 is useful. In most of the cases you
get this object from other objects.

AUTHOR

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

Returns the type of the motif.
(explain a little more)

seq

Returns the consensus sequence of the motif.

start

Returns the start position of the motif.

end

Returns the end position of the motif.

length

Returns the length of the motif.

get_id

Returns the primary ID of the motif. This is the internal ID from the MySQL database.

get_block

Return the multiple alignment block from which the motif
was generated.

Not yet implemented.

get_matrix

Returns the position frequency matrix of the motif.

Not yet implemented.
Return the sequence logo of the motif.

Not yet implemented.

get_subset_id

Returns the motif subset primary id.