NAME

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

VERSION

Version 0.5

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_subset_id

  Returns the motif subset primary id.

get_seqfeat_ids

  Returns all the sequence feature primary ids.