Endre Sebestyen
and 1 contributors

NAME

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

VERSION

Version 0.10

SYNOPSIS

  my $seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");
  my $type = $seqfeat->get_type;

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

Creates a new sequence feature object from the sequence feature primary id.

Return type: Bio::DOOP::SequenceFeature object

  $seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");

get_id

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

get_score

This method is not yet implemented.

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

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".