> In article <browns02-3010961305560001 at mcrcr1.med.nyu.edu>,
> Stuart M. Brown <browns02 at mcrcr.med.nyu.edu> wrote:
> >We are doing a bunch of BLAST searches with the EST database.
> >
> >I just got an idea - since these est's are routinely BLASTed
> >before they are submitted- and these results are generally noted
> >in the comment field, why can't I search the EST database for
> >comments that mention BLAST hits against my sequences of interest?
> >
> >I've tried LOOKUP- but the "All text" field does not appear to
> >include the comment field of the GenBank entry. I also
> >tried ENTREZ with only a bit more success - yet I can see mentions
> >of my sequence in the comments when I do my own BLAST searches and
> >then read the full annotation of the ESTs that we hit.
In article <558p26$pgc at dismay.ucs.indiana.edu>, gilbertd at bio.indiana.edu
(Don Gilbert) wrote:
> Stuart,
>> This may be a function of how SRS (or the GCG variant Lookup) is
> configured at a particular server. At IUBIo Archive, I revised the
> indexing for SRS to make sure the Genbank comment fields were
> searchable. As a test of your question, I just now searched
> the Genbank EST section at IUBIo, searching "Comment" fields
> for "BLAST", and found 165 matches.
>> Feel free to use this SRS server for Genbank lookups.
>http://iubio.bio.indiana.edu:81/srs/srsc>> - Don
>> -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu
----------------------------------------------
Don, You found only 165 ESTs that mention "BLAST" in the comment field???
I believe that virtually all ESTs are BLAST searched before being
submitted to the database, and I have heard a statistic that about 40% of
them find one or more significant hits. You should get hundred of
thousands of hits, no?
Where is this information stored if it is not in the comment or
description fields??
--
Stuart M. Brown, Molecular Biology Consultant
NYU-MC Research Computing Resource, Dept. of Cell Biology
550 First Ave, New York, NY 10016
Phone: (212)263-7689 FAX: (212)263-8139
