NAME

  Bio::DOOP::Sequence - Promoter sequence object

VERSION

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, 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

get_all_subsets

  Return the subset that is contain this sequence

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP