Frequency of BstE II cutting?

Mikhail Alexeyev malexeyev at biost1.thi.tmc.edu
Tue Jul 2 16:59:41 EST 1996


In article <4rasu5$mb6 at scotsman.ed.ac.uk>, chrisb at hgu.mrc.ac.uk (Chris
Boyd) wrote:

> Mikhail Alexeyev (malexeyev at biost1.thi.tmc.edu) wrote:
 (snip)

> : Very true, but the original post implied to DISREGARD these considerations
> : by asking to compare frequency of BstEII cutting with that of a generic
> : six-cutter (1 in 4096 disregarding sequence distribution considerations),
> : didn't it? 
> 
> Mikhail, I realised that, but I thought it would be useful to give some
> extra relevant information.  In particular, I took the original
> poster's caveat about sequence distributions to refer to the substrate
> DNA, not the recognition sequence.  I was pointing out (inter alia)
> that you have to take account of the recognition sequence also, even if
> the substrate DNA is constant and of random sequence.  In such a
> substrate, for example, BssHII (GCGCGC) sites will occur more
> frequently than BstEII sites.
> 
 
Chris, I must disagree.  
First, BOTH you and Bill refer to substrate DNA. Let me quote you:

> : > In reality, however, the occurrence
> : > frequency of any given query sequence is markedly affected by the base
> : > composition and sequence microstructure (CpG islands etc.) of the
> : > target DNA.

Second, although I am not sure what do you mean by constant DNA, from
everything mentioned in this thread so far and from quick glance at two
articles you are referring to I do not see why BstEII would cut not as
frequent as BssHII in a RANDOM sequence. Success of Markov chain analysis
(2-nd order and up) is in the fact that it takes advantage of
experimentally determined nonrandomness of nucleotide distribution. If
sequence is really random, this correction (I think) will not be
necessary. 

 In general, I beleive that composition of recognition sequence is
secondary to genome structure and may be ignored.

Regards,
M.A.



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