Path: utzoo!attcan!uunet!bionet!bionet-20.bio.net!GOAD.DAVISON
From: GOAD.DAVISON@BIONET-20.BIO.NET (Dan Davison)
Newsgroups: bionet.general
Subject: biological analysis algorithms
Message-ID: <12503227250.13.GOAD.DAVISON@BIONET-20.BIO.NET>
Date: 19 Jun 89 00:38:36 GMT
Sender: daemon@NET.BIO.NET
Lines: 42


   [T]he reviewer notes that little information is provided on the
   Algorithms and actual methods used by computers.  Could some one 
   suggest a good book covering these areas.

The Bionet mailer didn't believe the poster's addresss, so I'm posting this
to Bionet-News.

There are a number of excellent works that review the algorithms
mentioned by Lesk.

First and foremost is the CRC Press book, edited by Mike Waterman,
called "Mathematical Methods for DNA Sequences".  The only drawback
to this book is its price, about $150.0

Gunnar von Heijne has a book whose title is something like
"Biological Sequence Analysis" and whose subtitle is the memorable
"Treasure Trove or Trivial Pursuit".  It covers most of the methods
a molecular biologist would want to use.  I reviewed it recently
in Mathematical Biosciences.  He reviews the algorithms and their
weaknesses; the book's main problem is that it does not cover the
alignment algorithms well.

Depending on your taste, there are some reviews to note on sequence
alignment algorithms.  The first  is Mike Waterman's review in 
the Bulletin of Mathematical Biology, 1984, 46(4):473-500, "General
Methods of Sequence Comparison".  Next I would put Seller's
"The Theory and Computation of Evolutionary Distances: Pattern
Recognition" J. Algorithms 1:359-373, 1980.  Lastly, there is
an excellent book edited by David Sankoff and Joseph Kruskal,
"Time warps, string edits, and macromolecules: The theory and practice
of String Comparison" (Addison-Wesley, Reading, MA) 1983.

I had a review a while back in the Bulletin of Mathematical Biology,
1985, "Sequence Similarity ('Homology') Searching for Molecular
Biologists" 47(4):479 (I think).  It compared implementations of
search algorithms and was intended to complement the Waterman
review.

dan davison/theoretical biology/ los alamos national laboratory/
t-10 ms k710/los alamos nm 87545 USA/dd@lanl.gov/davison@uhou (bitnet)
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