Provided by: libbio-perl-perl_1.7.2-2_all bug


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


           $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');

           # 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');


       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.


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AUTHOR - Ewan Birney



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

        Title   : get_Seq_by_id
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : get_Seq_by_acc
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : guess_id
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : use_database
        Usage   :
        Example :
        Returns :
        Args    :