[Biojava-l] Parse error with negative strand CDS

[Schreiber, Mark]

Hi -

This looks odd. It may be that the Genbank produced by VectorNTI is not quite right. Can you post the file, or at least the few lines surrounding the CDS feature?

- Mark


-----Original Message-----
From: Criscuolo, Fred [mailto:fred.criscuolo at pfizer.com] 
Sent: Friday, 12 September 2003 4:27 a.m.
To: 'biojava-l at biojava.org'
Subject: [Biojava-l] Parse error with negative strand CDS


Hi,
I am using BioJava 1.3.0 to process a GenBank file that has a CDS on the negative strand. I am using the SeqIOTools.readGenbank(BufferedReader)
method to parse the file. I get the following error for any CDS on the negative strand:

  This line could not be parsed:  CDS            complement(518..1597)

The GenBank files I'm working with are produced by the VectorNTI application. I'm using Java 1.4.2.  I've searched the biojava mailing list but have not seen a reference to this particular problem. Any idea what's wrong? Thanks. Fred

Fred Criscuolo
Research Informatics - Pfizer, Inc.
858.622.7307 



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