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Subject: CSLG|COMMENTARY: From Andrew Coulson
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Date: Fri, 4-Dec-87 22:27:52 EST
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Posted: Fri Dec  4 22:27:52 1987
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From: Sunil Maulik 

 4-Dec-87 12:33:43-PST,9076;000000000001
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From:       A.F.W.Coulson@EDINBURGH.AC.UK
Subject:    CSLG Discussion or Conference
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Message-ID: <04 Dec 87  20:28:06 gmt  100798@EMAS-A>

       Searching large databases for sequence similarities.

       As far as the molecular biologist user is concerned, the important point
about this efficiency is that it is practicable to perform exhaustive searches
repeatedly and interactively; our experience is that database searching is not
best regarded as a one-off process -- much more of biological value is to be
found by modifying search conditions (changing scoring schemes, limiting the
search to some regions of the query sequence or the database, etc) in the light
of the results obtained with the first set of conditions used.
       The appropriate measure of efficiency in computing terms is the cost of
doing the calculation.  This summer we were able to make one comparison in
a particularly straightforward way, by running a search using FASTP on a VAX,
and using our program on a DAP in the Edinburgh Regional Computing Centre.
The point was that ERCC sold computing time on both types of machine on
essentially the same basis as far as their financial accounting was
concerned, so we could turn the cpu times into strictly comparable sums of
money.  It turned out that the exhaustive search was not only better and
faster than FASTP, but actually slightly cheaper.  I should say of course that
ERCC is not a commercial operation, and that academic users at Edinburgh do
not have to find real money for their use of the Centre's facilities; also that
the terms on which ERCC acquired the two machines are not comparable:
the only firm conclusion I want to argue is that it is quite clear that
exhaustive searches on the appropriate architecture are at least comparable
in cost to slower, approximate searches on conventional machines of inappropriat
architecture.
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