NAME
Bio::DOOP::Sequence - Promoter sequence objectVERSION
Version 0.06
SYNOPSIS
DESCRIPTION
This object represent the promoters in the database.
You can access the different annotation through this
object.AUTHOR
Tibor Nagy, Godollo, HungaryMETHODS
new
$seq = Bio::DOOP::Sequence->new($db,"1234");
The arguments is the following: Bio::DOOP::DBSQL object, primary idget_id
Return the sequence primary id. It is the MySQL idget_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 fileget_length
Return the length of the sequenceget_date
Return the modification date of the MySQL recordget_ver
Return the version of the sequenceget_annot_id
Return the annotation primary id. Is is used by the MySQL querysget_orig_id
This is not yet usedget_data_id
Return the sequence data primary id. Is is used by the MySQL querysget_taxon_id
Return the taxon annotiation primary id. Is is used by the MySQL querysget_data_main_db_id
Return the sequence annotation data primary id. Is is used by the MySQL querysget_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 emptyget_fasta
print $seq->get_fasta;
Print out the promoter sequence in FASTA formatget_blast
print $seq->get_blast;
Print out the Blast resultget_taxid
$taxid = $seq->get_taxid;
Return the NCBI taxid of the sequenceget_taxon_name
print $seq->get_taxon_name;
Print out the taxon name of the sequenceget_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 sequenceprint_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 namesget_xref_value
@values = @{$seq->get_xref_value("go_id")};
Return the arrayref of the values that contains the specified database nameget_all_seq_features
@seqfeat = @{$seq->get_all_seq_features};
Return the arrayref of all sequence featuresget_all_subsets
Return the subset that is contain this sequence