[Biojava-l] Problems parsing in RNA sequence in genbank format

Schreiber, Mark mark.schreiber at agresearch.co.nz
Sun Apr 6 19:12:15 EDT 2003

Hi -
Ambiguity other than N was not supported for RNA until very recently in biojava. Biojava live should contain the update and it will be released in bj1.3
- Mark

	-----Original Message----- 
	From: Lachlan Coin [mailto:lc1 at sanger.ac.uk] 
	Sent: Sat 5/04/2003 1:02 a.m. 
	To: biojava-l at biojava.org 
	Subject: [Biojava-l] Problems parsing in RNA sequence in genbank format

	I am parsing in RNA sequence data.  One of the positions has a 'R' which
	stands for the ambiguity symbol A or G.  However, the RNA alphabet does
	not have this as a token for anything (I did a quick test, and the
	ambiguity token for A or G is N).  So the genbank reader falls over when
	it gets to this.
	Any suggestions on how to handle this?  Can we modify the symbol
	tokenization for RNA to cope with this case?
	Thanks a lot,
	Biojava-l mailing list  -  Biojava-l at biojava.org

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