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: <4309@ig.ig.com> Date: Fri, 4-Dec-87 22:34:35 EST Article-I.D.: ig.4309 Posted: Fri Dec 4 22:34:35 1987 Date-Received: Thu, 10-Dec-87 01:49:43 EST Sender: daemon@presto.ig.com Lines: 46 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. Since Alex Reisner has mentioned transputers, I would extend what he say somewhat:- Viewed as a general purpose computing machine, a single T800 has comparable power to a VAX (?750 ?780); the NWS algorithms for a single pairwise comparison will run in a practicable time on a VAX. So the database search problem can be farmed out to a heap of transputers, using one for each pairwise comparison. If you have 1000 transputers (the planned size of the Edinburgh Concurrent Supercomputer; the first 200 are being installe at present), and 6000 sequences in the database, each machine only has to do six jobs. So the problem can be mapped in a simple way onto ECS, and no doubt we shall do some searches this way, because why not? But this application (as I've said already) doesn't use the general purpose computing facilities of the transputer processor, so though it may be an effective solution, it will not be a cost-effective one compared to the DAP. Of course, this may not matter to individuals who do not themselves have to find the true economic cost of the computing they do...... I don't know much about the Connection Machine apart from what I read i Scientific American, but I think a similar point may apply. As I understand it, it will be possible to use a similar mapping to that used in the DAP search program on the Connection Machine, but the only communication this needs is between each node and two neighbours, so that the expensively-provided richness and flexibility of interconnection may not be used very effectively. As I say, I don't know much about it, and if anybody has an idea for mapping the problem in a way which makes better use of the particular strengths of this machine (or of a transputer array), I shall be interested to hear it. -------