Multiple alignment of protein sequences

doelz at doelz at
Fri Feb 7 05:13:35 EST 1992

In article <1992Feb6.141356.9142 at>, WEISE at (MICHAEL WEISE) writes:

> In trying to decide between meaningful homology and garbage, also note that
> GCG7's BESTFIT has an optional parameter ( /RANDOMIZE=n ) that provides a mean
> and for n comparisons where one of the sequence pair is randomized. 
> If the score for the nonrandom alignment is 'significantly' greater than the

True, true. But remember that statistical significance must not necessarily
reflect what you consider to be biological significance. I remember that there
was an old paper of Lipman et al in the middle 80's on statistical problems 
in the sequence comparison field. While BESTFIT's randomize is rather crude 
I should recommend W.Pearson's RDF2 which also permits to suffle *windows*
of the sequence, thus leaving the sequence more intact than the pure 
monte carlo would permit. RDF2 is described in various papers including 
Pearson and Lipman, PNAS (1988) 85:2444-2448, and available from William 


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