Relay-Version: version B 2.10 5/3/83; site utzoo.UUCP Path: utzoo!utgpu!water!watmath!uunet!ig!daemon From: daemon@ig.UUCP Newsgroups: bionet.molbio.news Subject: CSLG|COMMENTARY: From Andrew Coulson Message-ID: <4308@ig.ig.com> Date: Fri, 4-Dec-87 22:27:52 EST Article-I.D.: ig.4308 Posted: Fri Dec 4 22:27:52 1987 Date-Received: Thu, 10-Dec-87 01:48:20 EST Sender: daemon@presto.ig.com Lines: 43 From: Sunil Maulik4-Dec-87 12:33:43-PST,9076;000000000001 Return-Path: <@WISCVM.WISC.EDU:A.F.W.Coulson@EDINBURGH.AC.UK> Received: from WISCVM.WISC.EDU by BIONET-20.ARPA with TCP; Fri 4 Dec 87 12:33:28-PST Received: from UKACRL.BITNET by WISCVM.WISC.EDU ; Fri, 04 Dec 87 14:34:41 CDT Received: from RL.IB by UKACRL.BITNET (Mailer X1.25) with BSMTP id 1126; Fri, 04 Dec 87 20:27:53 GMT Via: UK.AC.RL.EARN; Fri, 04 Dec 87 20:27:52 GMT Received: Via: 000015001006.FTP.MAIL; 4 DEC 87 20:27:44 GMT Date: 04 Dec 87 20:28:06 gmt From: A.F.W.Coulson@EDINBURGH.AC.UK Subject: CSLG Discussion or Conference To: MAULIK%arpa.bionet-20%RL.earn 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. -------