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Endre Sebestyen > Bio-DOOP-DOOP > Bio::DOOP::SequenceFeature

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Bio-DOOP-DOOP-1.04.tar.gz

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Module Version: 0.10   Source  

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".

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