[Biojava-l] parsing mRNA GenBank flat file

[Matthew Pocock]

Mark: Do RNA Genbank entries use agcu? RNA embl entries use DNA (agct) 
to serialise the sequence.

Alexander: Could you give us an accession number that causes this error 
as well as the error you get? The complete stack trace is always helpful 
for fixing things.

Matthew

Schreiber, Mark wrote:
> The problem is probably being caused by the use of the DNA alphabet
> instead of the RNA alpahbet. Are you getting IllegalSymbolExceptions?
> 
> If this is the case you need to use the RNA alphabet in the GenBank
> parser this can be found by calling RNATools.getRNA();
> 
> - Mark
> 
> 
>>-----Original Message-----
>>From: Alexander Churbanov [mailto:achurbanov@yahoo.com] 
>>Sent: Thursday, 16 May 2002 1:56 p.m.
>>To: biojava-l@biojava.org
>>Subject: [Biojava-l] parsing mRNA GenBank flat file
>>
>>
>>   Hello,
>>
>>   I am trying to parse mRNA file from Gen Bank using
>>your demo program (That parses DNA GenBank flat file).
>>It crashes on the halfway or at the beginning. Do you
>>have any suggestions, other methods, demo programs or
>>other sources showing how to do it.
>>   Thanks in advance,
>>
>>   Alexander Tchourbanov
>>
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> 
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