[BioC] Help with genbank

Jeff Gentry jgentry at jimmy.harvard.edu
Thu Mar 6 15:09:12 MET 2003

> I would like to extract the sequence information corresponding to an
> accession number.  I use the function in annotate 
> x <- genbank("AK008608")
> to extract the XML file and hope someone can point me to some functions
> (or directions) to further extract the sequence info from
> x$doc$childern.

Unfortunately we don't really have any notion of a genbank object like we
do with pubmed (the pubMedAbst class), nor have any convenience functions
to go in and retrieve that information.

I'm not familiar enough w/ the XML structures to say which parts
correspond to what you're looking for, but if you look at functions like
buildPubMedAbst it can show you how to get at the pieces that you want.


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