Bio::DOOP::SequenceFeature - Object for the sequence features
Version 0.07
This object gives access to the sequence features ( conserved motif, repeat, CpG island, TFBS and TSS annotation ).
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
$seqfeat = Bio::DOOP::SequenceFeature->new($db,"112"); You can create the object with the new method. The arguments are the following : Bio::DOOP::DBSQL object, sequence_feature_primary_id
Returns the primary ID of the feature. This is the internal ID from the MySQL database.
Returns the score of the feature. We don't really need this now.
Returns the start position of the feature.
Returns the end position of the feature.
Returns the length of the feature. Return type: string
Nothing to see here. Move along.
Returns the sequence of the feature.
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
Returns the motif primary ID, if the feature type is "con".
Returns the tfbs primary ID, if the feature type is "tfbs".
Returns the cpg primary ID, if the feature type is "cpg".
Returns the repeat primary ID, if the feature type is "rep".
Returns the ssr primary ID, if the feature type is "ssr".
Returns the tss primary ID, if the feature type is "tss".
Returns the primary ID of the sequence containing this feature.
Returns the subset primary ID of the feature, if the feature type is "con".
$motif = $seqfeat->get_motif; Returns the motif object associated with the feature. If the feature type is not "con" this value is NULL.
Returns the tss type, if the feature type is "tss".
Returns the tss id, if the feature type is "tss".
Returns the description of the tss, if the feature type is "tss".
Returns the xref of the tss, if the feature type is "tss".
To install Bio::DOOP::DOOP, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DOOP::DOOP
CPAN shell
perl -MCPAN -e shell install Bio::DOOP::DOOP
For more information on module installation, please visit the detailed CPAN module installation guide.