[Biojava-l] Genbank ASN.1 or XML parser

Gang Wu gwu at molbio.mgh.harvard.edu
Thu Jun 3 12:52:52 EDT 2004


I would be glad to write the parser. Since I am pretty new to BioJava
project, can anybody give me a guide on how to start? Thanks.

- Gang

-----Original Message-----
From: mark.schreiber at group.novartis.com
[mailto:mark.schreiber at group.novartis.com]
Sent: Wednesday, June 02, 2004 8:59 PM
To: gwu at molbio.mgh.harvard.edu
Cc: Bio-Java; biojava-l-bounces at portal.open-bio.org
Subject: Re: [Biojava-l] Genbank ASN.1 or XML parser

Hello -

At the moment there are no parsers for XEMBL, GenBankXML or ASN.1, They
could both be easily made if someone had that time. GenBankXML could
easily draw on a SAX or DOM parser to pass events to the BioJava
SequenceBuilders (using some kind of adapter). ASN.1 would need a more
custom parser but because it is highly structured that shouldn't be too

Any volunteers?

- Mark

"Gang Wu" <gwu at molbio.mgh.harvard.edu>
Sent by: biojava-l-bounces at portal.open-bio.org
06/02/2004 11:21 PM
Please respond to gwu

        To:     "Bio-Java" <biojava-l at biojava.org>
        Subject:        [Biojava-l] Genbank ASN.1 or XML parser

Hi everyone,

I just tried out the APIs for parsing Genbank format files. Though it
well, I still wonder if there are APIs for parsing Genbank files in ASN.1
XML formats because the Genbank format was designed for human being and
ASN.1 and XML formats should be more reliable for data exchange.

Gang Wu

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