Z-Score and cutoff in protein sequence alignment

Arne Elofsson arne at hodgkin.mbi.ucla.edu
Thu May 4 17:15:42 EST 1995

In article <3o8j17$jrs at vixen.cso.uiuc.edu> xhu1 at ux1.cso.uiuc.edu (hu xiche) writes:
>         I am using the BESTFIT program in the GCG package to align two
> protein sequences.  I would like to evaluate the statistical significance
> of such an alignment.  By using the -RAND option, I can get the averaged
> quality of the "shuffled" random sequences and the standard deviation from
> the output of BESTFIT.  But I don't know how to convert them into
> "Z-score".  I will deeply appreciate your help in answering the following
> questions: (1) How should the "Z-Score" be calculated? and (2) What is the
> cutoff for statistically meaningful alignment in terms of "Z-Score"?
> Any references to published journal articles or names of experts who will
> be able to help will be very helpful.
>         Thanks in advance,
>         Xiche Hu

Z-sc = (Score - average)/ (stdev)

Z-score of 7 is correct. 5 is a probable hit.


               From: Arne Elofsson
         Email: arne at hodgkin.mbi.ucla.edu   			
  WWW:  http://www.doe-mbi.ucla.edu/arne/main.html	

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