From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena@)
Newsgroups: bionet.info-theory
Subject: DNA sequence alignment by maximum likelihood
Keywords: DNA sequence alignment maximum likelihood
Date: 16 Apr 92 23:14:57 GMT
Organization: Dept. of Crop Science, NCSU, Raleigh, NC.
Originator: samodena@csemail.cropsci.ncsu.edu

Earlier this week I attended a nice seminar given by Jeff Thorne. 
Two recent articles:

        An Evolutionary Model of Maximum Likelihood Alignment of 
                DNA Sequences
        J.L. Thorne, H. Kishino and J. Felsenstein
        J Mol Evol (1991) 33:114-124

ABSTRACT: Most algorithms for the alignment of biological 
sequences are not derived from an evolutionary model. 
Consequently, these alignment algorithms lack a strong 
statistical basis. A maximum likelihood method for the alignment 
of two DNA sequences is presented.  This method is based upon a 
statictical model of DNA sequence evolution for which we have 
obtained explicit transition probabilities.  The evolutionary 
model can also be used as the basis of procedures that estimate 
the evolutionary parameters relevant to a pair of unaligned DNA 
sequences.  A parameter-estimation approach which takes into 
account all possible alignments between two sequences is 
introduced; the danger of estimating evolutionary parameters 
from a single alignment is discussed."



        Inching toward Reality: An Improved Likelihood Model of 
                Sequence Evolution
        J.L. Thorne, H. Kishino and J. Felsenstein
        J Mol Evol (1992) 34:3-16

ABSTRACT: "Our previous evolutionary model is generalized to 
permit approximate treatment of multiple-base insertions and 
deletions as well as regional heterogeneity of substitution 
rates.  Parameter estimation and alignment procedures that 
incorporate these generalizations are used to access the accuracy 
of the parameter estimation procedure and an example of an 
inferred alignment is included."

Perhaps what I like most was that the two sequences tentively 
aligned were the 1552-bp 16S rRNA of Chlamydia psittaci and the 
1535-bp 16S rRNA of a mycoplasma-like organism (species not 
cited).  

Of course, since this is a maximum likelihood method, multi-
sequence alignment awaits invention of the next generation of 
supercomputers.

Jeff has a background in both molecular biology and statistics.  
I mentioned the bionet.info-theory forum to him (he knows what 
Internet is [jeff@amanita.cit.cornell.edu]).  Maybe he can be 
persuaded to join the conversation.  I sent him a copy of the
bionet.info-theory FAQ.

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