insertion/deletion:how to weigh in a DNA sequence matrix?

[Arlin Stoltzfus]

newsmgr at merrimack.edu (Andrew Roger) wrote:
> 
> Just to add another comment.  One should not consider all events of
> insertion and deletion to be occurring at the same rate.  It looks as
> though long insertions and deletions are probably much rarer events than
> short ones.  For an interesting study of the relative frequencies of
> insertions and deletions of various sizes see:
> 
> Gu and Li, J. Mol. Evol. 40: 464-473 (1995)
> 
> In this paper they suggest that the frequencies of insertions and
> deletions are described well by a power law:
> 
> Fk = Ck^-b

Yeah, and another interesting thing is that deletions in pseudogenes
are something like an order of magnitude more common than insertions,  
surely due to the fact that DNA polymerases generally cause 
more deletion mutations than insertion mutations.  The indels 
are strongly biased toward short lengths, as Andrew says, so that
whereas we might expect 66.6% of them to be frameshifts, the actual 
value is something more like 75% because most of the indels are 
just 1 or 2 bp.  All of this just goes to show that we take a great 
risk when we assume that mutations are uniformly distributed.  

I can provide some more references on what the spectrum of spontaneous 
mutations actually looks like, if people are interested.  

Arlin
-- 
Arlin Stoltzfus, Ph.D. (arlin at is.dal.ca)
Department of Biochemistry, Dalhousie University
Halifax, Nova Scotia B3H 4H7 CANADA
phone: 902-494-2968     fax: 902-494-1355