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
Inspired by Lincoln Stein, written by Ewan Birney.
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to one of the Bioperl
mailing lists. Your participation is much appreciated.
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive
experts will be able look at the problem and quickly address it. Please
include a thorough description of the problem with code and data examples if
at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs
and their resolution. Bug reports can be submitted via the web:
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : get_Seq_by_id
Title : get_Seq_by_acc
Title : guess_id
Title : use_database