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From: PEARSON@SUMEX-AIM.ARPA
Newsgroups: net.micro
Subject: IBM vs VAX/unix
Message-ID: <16959@sri-arpa.UUCP>
Date: Sun, 26-Feb-84 18:25:38 EST
Article-I.D.: sri-arpa.16959
Posted: Sun Feb 26 18:25:38 1984
Date-Received: Fri, 2-Mar-84 13:26:39 EST
Lines: 44

From:  William Pearson 


	Since I was surprised by these results, I thought I would share
them.  Those of you who compare benchmarks may find them interesting.

	I have been working on a program that compare the amino
acid sequence of a protein (a character string from a 20 letter
alphabet, the strings are usually from 100 - 500 characters long)
against a data bank of all known protein sequences in order to
identify unknown sequences and look for evolutionary relationships.
The data bank includes about 2500 sequences totalling 500,000
characters.  The problem is a dificult one, since related proteins
will have both substitutions and insertions or deletions.  The most
rigorous algorithms require n*n in time and space, we have been using
a much faster algorithm that uses a hashing technique and both the time
and space required are much less.

	The program was written in 'C' for porting between many small
machines, initially on a VAX 11/780 unix system.  It is also now running
on an IBM-PC with a 320K RAM disk.  The program was compiled with the
Lattice 'C' compiler.

Execution times for a 146 character sequence vs 190K databank subset.
(it has to fit on a floppy!)

VAX 11/780	1:17.4
IBM-PC		6:58		the databank was stored on the RAM disk,
				using the floppy takes about 2 min more.

I am now tempted to think of "1/2 of a VAX" as simply 3 IBM-PC's.

	On another subject, a salesman from a high performance work-
station manufactuer informs me that the Motorola 68020 will be available
"off-the-shelf" in 3 months.  This seems to conflict with discussions
on the relative merits of the 16032 vs 68020 which have suggested
the 68020 was not off the drawing board (screen?).  Since we are in
the market for a machine using this technology, and have not been able
to find a manufacturer who is shipping 16032 systems yet (one
hears a lot about 1Q 84), perhaps the 68000 series is not dead yet.

Bill Pearson

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