NAME
Bio::DOOP::Sequence - Promoter sequence object
VERSION
Version 0.01
SYNOPSIS
DESCRIPTION
This object represent the promoters in the database.
You can access the different annotation through this
object.
AUTHOR
Tibor Nagy, Godollo, Hungary
METHODS
new
$seq = Bio::DOOP::Sequence->new($db,"1234");
The arguments is the following: Bio::DOOP::DBSQL object, primary id
get_id
Return the sequence primary id. It is the MySQL id
get_fake_id
Return the fake gi.
get_db_id
Return the data primary id. Is is used by the MySQL querys and it is the header of the subset FASTA file
get_length
Return the length of the sequence
get_date
Return the modification date of the MySQL record
get_ver
Return the version of the sequence
get_annot_id
Return the annotation primary id. Is is used by the MySQL querys
get_orig_id
This is not yet used
get_data_id
Return the sequence data primary id. Is is used by the MySQL querys
get_taxon_id
Return the taxon annotiation primary id. Is is used by the MySQL querys
get_data_main_db_id
Return the sequence annotation data primary id. Is is used by the MySQL querys
get_utr_length
$utr_length = $seq->get_utr_length;
Return the length of the UTR contained by the sequence.
get_desc
print $seq->get_desc,"\n";
Print out the sequence description. Contain useful informations
from the sequence.
get_gene_name
$gene_name = $seq->get_gene_name;
Return the gene name of the promoter. If the gene is
unknow or not annotated, it is empty
get_fasta
print $seq->get_fasta;
Print out the promoter sequence in FASTA format
get_blast
print $seq->get_blast;
Print out the Blast result
get_taxid
$taxid = $seq->get_taxid;
Return the NCBI taxid of the sequence
get_taxon_name
print $seq->get_taxon_name;
Print out the taxon name of the sequence
get_taxon_class
print $seq->get_taxon_class;
Print out the taxonomical class (most of the cases it is the family)
of the species of the sequence
print_all_xref
$seq->print_all_xref;
Print out all the alternative database connections. It is contain
the GO id, NCBI RNA GI and so on. You use this method for debug your database.
get_all_xref_keys
@keys = @{$seq->get_all_xref_keys};
Return the arrayref of the alternative database names
get_xref_value
@values = @{$seq->get_xref_value("go_id")};
Return the arrayref of the values that contains the specified database name
get_all_seq_features
@seqfeat = @{$seq->get_all_seq_features};
Return the arrayref of all sequence features