Path: utzoo!attcan!uunet!yale!cmcl2!phri!roy
From: roy@phri.UUCP (Roy Smith)
Newsgroups: sci.bio
Subject: Re: Restriction Mapping and Software and Theory...
Keywords: DNA and maps...
Message-ID: <3529@phri.UUCP>
Date: 4 Oct 88 01:54:06 GMT
References: <21491@cornell.UUCP>
Reply-To: roy@phri.UUCP (Roy Smith)
Organization: Public Health Research Inst. (NY, NY)
Lines: 23

In article <21491@cornell.UUCP> wayner@cs.cornell.edu (Peter Wayner) writes:
> Does anyone have any references on software to do restriction mappings of
> DNA? Has anyone looked at the problem mathematically?  Has anyone looked
> at the problem from the standpoint of a computer scientist?

	Which problem are you talking about?  Given the lengths of the
fragments resulting from single and multiple digests construct a classical
restriction map, or given a sequence find all the restriction sites in it?
If it's the former, I can't help you much.

	If it's the latter, what you want to do is wait for the next issue
of Computer Applications in the Biosciences in which I have a paper
describing an algorithm for doing this in time proportional to the length of
the sequence and independent of the number of restriction enzymes.  To the
best of my knowledge, it beats the pants of any other currently available
algorithms.  To be fair, Mount and Conrad (Nucleic Acids Research (1986)
14:443-454) make mention of a similar algorithm, but unfortunately do not
describe the algorithm in any detail.
-- 
Roy Smith, System Administrator
Public Health Research Institute
{allegra,philabs,cmcl2,rutgers}!phri!roy -or- phri!roy@uunet.uu.net
"The connector is the network"