[Biojava-l] parse protein sequences in GenBank format

Cox, Greg gcox@netgenics.com
Tue, 27 Aug 2002 18:21:10 -0400

In short, yes.  The parsers need an alphabet to work with, and readGenbank()
is hard-coded to use the DNA alphabet.  If you look at the
SeqIOTools.readGenbank(), it depends on getDNAParser().  I saw readGenpept()
while looking around, which seems to be what you want.  That uses the
genbank format with an amino acid alphabet


-----Original Message-----
From: richard cai [mailto:cairi1@yahoo.com]
Sent: Tuesday, August 27, 2002 5:17 PM
To: biojava-l@biojava.org
Subject: [Biojava-l] parse protein sequences in GenBank format


I am trying to parse a flat file of refseq protein
sequences in what looks like GenBank format.  However,
although the program, using SeqIOTools.readGenbank()
and seq=seqs.nextSequence(), works fine with DNA
sequences in GenBank format, it fails to extract the
protein sequences.  Does this method of using
readGenbank() only deal with DNA sequences?



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