NAME

Bio::DB::Universal - Artificial database that delegates to specific databases

SYNOPSIS

    $uni = Bio::DB::Universal->new();
    # by default connects to web databases. We can also
    # substitute local databases
    $embl = Bio::Index::EMBL->new( -filename => '/some/index/filename/locally/stored');
    $uni->use_database('embl',$embl);
    # treat it like a normal database. Recognises strings
    # like gb|XXXXXX and embl:YYYYYY
    $seq1 = $uni->get_Seq_by_id("embl:HSHNRNPA");
    $seq2 = $uni->get_Seq_by_acc("gb|A000012");
    # with no separator, tries to guess database. In this case the
    # _ is considered to be indicative of swissprot
    $seq3 = $uni->get_Seq_by_id('ROA1_HUMAN');

DESCRIPTION

Artificial database that delegates to specific databases, with a "smart" (well, smartish) guessing routine for what the ids. No doubt the smart routine can be made smarter.

The hope is that you can make this database and just throw ids at it - for most easy cases it will sort you out. Personally, I would be making sure I knew where each id came from and putting it into its own database first - but this is a quick and dirty solution.

By default this connects to web orientated databases, with all the reliability and network bandwidth costs this implies. However you can subsistute your own local databases - they could be Bio::Index databases (DBM file and flat file) or bioperl-db based (MySQL based) or biocorba-based (whatever you like behind the corba interface).

Internally the tags for the databases are

   genbank - ncbi dna database
   embl    - ebi's dna database (these two share accession number space)
   swiss   - swissprot + sptrembl (EBI's protein database)

We should extend this for RefSeq and other sequence databases which are out there... ;)

Inspired by Lincoln Stein, written by Ewan Birney.

FEEDBACK

  bioperl-l@bio.perl.org

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

 Title   : get_Seq_by_id
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : get_Seq_by_acc
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : guess_id
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : use_database
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :