Tibor Nagy > Bio-DOOP-DOOP-1.02 > Bio::DOOP::SequenceFeature

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Module Version: 0.09   Source   Latest Release: Bio-DOOP-DOOP-1.04

NAME ^

  Bio::DOOP::SequenceFeature - Object for the sequence features

VERSION ^

Version 0.09

SYNOPSIS ^

DESCRIPTION ^

  This object gives access to the sequence features ( conserved motif, repeat, CpG island,
  TFBS and TSS annotation ).

AUTHORS ^

  Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

METHODS ^

new

  $seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");
 
  You can create the object with the new method.

  The arguments are the following : Bio::DOOP::DBSQL object, sequence_feature_primary_id

get_id

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

get_score

  Returns the score of the feature. We don't really need this now.

get_start

  Returns the start position of the feature.

get_end

  Returns the end position of the feature.

length

  Returns the length of the feature.

get_seq

  Returns the sequence of the feature.

get_type

  Returns the type of the feature. (con, ssr, tfbs, rep, cpg, tss).

  con  : evolutionary conserved non-coding region
  ssr  : simple sequence repeat
  tfbs : transcription factor binding site
  rep  : repeat
  cpg  : cpg island
  tss  : transcription start site

get_motifid

  Returns the motif primary ID, if the feature type is "con".

get_tfbsid

  Returns the tfbs primary ID, if the feature type is "tfbs".

get_cpgid

  Returns the cpg primary ID, if the feature type is "cpg".

get_repeatid

  Returns the repeat primary ID, if the feature type is "rep".

get_ssrid

  Returns the ssr primary ID, if the feature type is "ssr".

get_tssid

  Returns the tss primary ID, if the feature type is "tss".

get_seqid

  Returns the primary ID of the sequence containing this feature.

get_subsetid

  Returns the subset primary ID of the feature, if the feature type is "con".

get_motif

  $motif = $seqfeat->get_motif;

  Returns the motif object associated with the feature.
  If the feature type is not "con" this value is NULL.

get_tss_type

  Returns the tss type, if the feature type is "tss".

get_tss_id

  Returns the tss id, if the feature type is "tss".

get_tss_desc

  Returns the description of the tss, if the feature type is "tss".

get_tss_xref

  Returns the xref of the tss, if the feature type is "tss".
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