NAME

  Bio::DOOP::Sequence - promoter sequence object

VERSION

Version 0.12

SYNOPSIS

DESCRIPTION

  This object represents a specific promoter in the database.
  You can access the annotation and the sequence through this object.

AUTHORS

  Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

METHODS

new

  $seq = Bio::DOOP::Sequence->new($db,"1234");
  The arguments are the following : Bio::DOOP::DBSQL object, sequence_primary_id

new_from_dbid

  Create new objects form sequence primary id.

get_id

  $sequence_id = $sequence->get_id;

  Returns the sequence primary id. This is the internal ID from the MySQL database.
  Return type : string

get_fake_id

  $fake_id = $sequence->get_fake_id;

  Returns the sequence fake GI.
  Return type : string

get_db_id

  $db_id = $sequence->get_db_id;

  Returns the full sequence ID.
  Return type : string

get_length

  $length = $sequence->get_length;

  Returns the length of the sequence.
  Return type : string

get_date

  $date = $sequence->get_date;

  Returns the modification date of the MySQL record.
  Return type : string

get_ver

  $version = $sequence->get_ver;

  Returns the version of the sequence.
  Return type : string

get_annot_id

  $annotation_id = $sequence->get_annot_id;

  Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
  Return type : string

get_orig_id

  This method is not yet implemented.

get_data_id

  $data_id = $sequence->get_data_id;

  Returns the sequence data primary id. This is the internal ID from the MySQL database.
  Return type : string

get_taxon_id

  $taxon_id = $sequence->get_taxon_id;

  Returns the taxon annotation primary id. This is the internal ID from the MySQL database.
  Return type : string

get_data_main_db_id

  $data_main_db_id = $sequence->get_data_main_db_id;

  Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
  Return type : string

get_utr_length

  $utr_length = $seq->get_utr_length;

  Returns the length of the 5' UTR included in the sequence.
  Return type : string

get_desc

  print $seq->get_desc,"\n";

  Returns the description of the sequence.
  Return type : string

get_gene_name

  $gene_name = $seq->get_gene_name;

  Returns the gene name of the promoter. If the gene is
  unknow or not annotated, it is empty.
  Return type : string

get_fasta

  print $seq->get_fasta;

  Returns the promoter sequence in FASTA format.
  Return type : string

get_raw_seq

  print $seq->get_raw_seq;

  Returns the raw sequence without any other identifier
  Return type: string

get_blast

  This method is not yet implemented.

get_taxid

  $taxid = $seq->get_taxid;

  Returns the NCBI taxon ID of the sequence.
  Return type : string

get_taxon_name

  print $seq->get_taxon_name;

  Returns the scientific name of the sequence's taxon ID.
  Return type : string

get_taxon_class

  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.
  Return type : string

print_all_xref

  $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

get_all_xref_keys

  @keys = @{$seq->get_all_xref_keys};

  Returns the arrayref of xref names.

get_xref_value

  @values = @{$seq->get_xref_value("go_id")};

  Returns the arrayref of a given xref's values'.

get_all_seq_features

  @seqfeats = @{$seq->get_all_seq_features};

  Returns the arrayref of all sequence features or -1 in case of error.

get_all_subsets

  @subsets = @{$seq->get_all_subsets};

  Returns the subsets containing the sequence.
  Return type : arrayref, the array containig Bio::DOOP::ClusterSubset objects

cpanm Bio::DOOP::DOOP

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