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
Greg -----Original Message----- From: richard cai [mailto:[EMAIL PROTECTED]] Sent: Tuesday, August 27, 2002 5:17 PM To: [EMAIL PROTECTED] Subject: [Biojava-l] parse protein sequences in GenBank format Hello, 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? Thanks. Rich __________________________________________________ Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes http://finance.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
