Bio::DOOP::Sequence - promoter sequence object
Version 0.11
This object represents a specific promoter in the database. You can access the annotation and the sequence through this object.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
$seq = Bio::DOOP::Sequence->new($db,"1234"); The arguments are the following : Bio::DOOP::DBSQL object, sequence_primary_id
Create new objects form sequence primary id.
Returns the sequence primary id. This is the internal ID from the MySQL database.
Returns the sequence fake GI.
Returns the full sequence ID.
Returns the length of the sequence.
Returns the modification date of the MySQL record.
Returns the version of the sequence.
Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
This method is not yet implemented.
Returns the sequence data primary id. This is the internal ID from the MySQL database.
Returns the taxon annotation primary id. This is the internal ID from the MySQL database.
$utr_length = $seq->get_utr_length; Returns the length of the 5' UTR included in the sequence.
print $seq->get_desc,"\n"; Returns the description of the sequence.
$gene_name = $seq->get_gene_name; Returns the gene name of the promoter. If the gene is unknow or not annotated, it is empty.
print $seq->get_fasta; Returns the promoter sequence in FASTA format.
Returns the raw sequence without any other identifier Return type: string
print $seq->get_blast; This method is not yet implemented.
$taxid = $seq->get_taxid; Returns the NCBI taxon ID of the sequence.
print $seq->get_taxon_name; Returns the scientific name of the sequence's taxon ID.
print $seq->get_taxon_class; Returns the taxonomic class of the sequence's taxon ID. Used internally, to create monophyletic sets of sequences in an orthologous cluster.
$seq->print_all_xref; Prints all the xrefs to other databases. Type of xref IDs : go_id : Gene Ontology ID ncbi_gene_id : NCBI gene ID ncbi_cds_gi : NCBI CDS GI ncbi_rna_gi : NCBI RNA GI ncbi_cds_prot_id : NCBI CDS protein ID ncbi_rna_tr_id : NCBI RNA transcript ID at_no : At Number
@keys = @{$seq->get_all_xref_keys}; Returns the arrayref of xref names.
@values = @{$seq->get_xref_value("go_id")}; Returns the arrayref of a given xref's values'.
@seqfeat = @{$seq->get_all_seq_features}; Returns the arrayref of all sequence features or -1 in case of error
Returns the subset containing the sequence.
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.