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Using GO annotation in a blast reflib

Mark Waugh mew at ncgr.org
Wed Oct 4 10:39:27 PDT 2000


Hello,

We are interested in augmenting the sequence definitions in standard
Blast output with their corresponding GO annotations where available. To
do this, we can either create reflibs containing only those sequences
with GO annotations, or we can scan the HSPs resulting from a search
against either NT or NR for GB identifiers that have corresponding GOids
from the GO database. In either case it would seem to be a fairly
straightforward mapping between Genbank accessions and GOids. The
problem is that, although there is a place for Genbank accession numbers
in the table dbxref, there aren't any in the latest version of the
database (we have a local version running in house and obtained the
latest update on Tuesday from John Richter). We have experimented with
the idea of using a webbot to obtain the GB accession numbers from the
consortium members' individual web sites based on identifiers (the
contributing group's internal accession numbers) parsed from the
association files available on the GO website, and while this appears to
work, it's pretty convoluted and we don't want to flood these sites with
automated requests. This also introduces a potential problem of
synchronization between the version of GO we are running and all of the
ancillary files we are parsing to get the GB accessions.

Are there any plans in the near future to populate the dbxref table with
IC accession numbers, and if not, can anyone suggest where we might
obtain this information for each sequence represented in GO?

Thanks very much for your time.

Mark


-- 
Mark Waugh, Scientist 
National Center for Genome Resources
2935 Rodeo Park Drive East
Santa Fe, NM 87505, USA
mew at ncgr.org http://www.ncgr.org	
Ph: (505) 995-4446, (800) 450-4854 Fax: (505) 982-7690

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