Subject: RE: Sequence Classes and CORBA Servers

From: "David J. States" <[email-masked]>
Date: Wed, 12 Nov 1997 10:52:48 -0600

> 1) Are there any "standard" C++, Java or IDL specifications for
classes that
> represent
>     a) DNA sequences,
>     b) RNA sequences,
>     c) Protein sequences,
>     d) Pairwise and multiple sequence alignments?
> 
> 2) What's the relation of the above sequence class specifications to
existing
> flat-file sequence formats (EMBL, GenBank, PIR, SwissProt, ...)?
> 
> 3) Are there any CORBA servers available now ...

The NCBI does deliver sequence in ASN.1 format from their web site.
While ASN.1 is not CORBA, the NCBI bio-seq definitions are robust and
have been stable for a number of years.
The mapping from ASN.1 to CORBA is not as smooth as it might be because
many (the vast majority) of the fields in the ASN.1 definitions are
optional and not used in any particular entry.  I don't know what plans
NCBI has with regard to CORBA, but it would be worth asking them.
Alternatively, a JAVA class that loaded NCBI objects would be nice to
have.

David States
Institute for Biomedical Computing
Washington University