Frequency of BstE II cutting?

[Mikhail Alexeyev]

In article <4qubv9$188 at scotsman.ed.ac.uk>, chrisb at hgu.mrc.ac.uk (Chris
Boyd) wrote:

> Mikhail Alexeyev (malexeyev at biost1.thi.tmc.edu) wrote:
> : In article <DtIG58.8wK.B.midge at bath.ac.uk>, bspwrb at bath.ac.uk (W R
> : BENNETT) wrote:
> 
> : > If BstE II has a restriction site of GGTNACC, does it cut at the same
> : > frequency as a six-cutter (i.e. an average 1 in 4096 disregarding sequence
> : > distribution considerations), which is the "intuitive" answer, or does it
> : > cut with reduced frequency (which is what I'd like!).  Promega's technical
> : > department felt that it definitely cut at reduced frequency, but couldn't
> : > really say why, or what the frequency was.... 
> :  
> 
> 
> : Yet another way to put it is in terms of probability to encounter a
> : specific nucleotide at a specific position. For BstEII it should be:
> 
> :  G   G   T   N   A   C   C
> : 1/4 1/4 1/4 4/4 1/4 1/4 1/4
> 
> : Probability is: (1/4)^6 x 4/4= 4^-6= 1 in 4096
> 
> Yes, this is a fair first approximation way of looking at this, and is
> all you need for most applications. 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.  E.g., CTAG is far rarer than GATC in the E. coli genome.
> 
> For pedantically accurate theoretical results, you unfortunately have
> to do a Markov chain analysis to explain why, and calculate to what
> extent, sequences with repeated adjacent bases are commoner than the
> above naive analysis would suggest.
> 
 


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? 


M. Alexeyev













































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