Author image Endre Sebestyen
and 1 contributors

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}