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Bio::DB::Universal(3pm) User Contributed Perl Documentation Bio::DB::Universal(3pm)


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
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 Title   : get_Seq_by_acc
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 Title   : guess_id
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 Title   : use_database
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2018-10-27 perl v5.26.2