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Iterative GAP with tabulated output???

Arle Kruckeberg arle at biovax.leeds.ac.uk
Sun Jan 22 15:05:57 EST 1995


Dear GCG whizzes:

I am studying a family of homologous proteins from diverse organisms. I
would
like to produce a table that includes % identity and similarity,
Needleman and Wunsch (GAP) alignment quality and the quality +-
standard deviation of x randomizations, and the number of gaps
introduced to produce each alignment. In other words, to run GAP lots
of times, on a list of file names, and put the numerical output into a
separate file (and leave the sequence alignment to PILEUP). Is this
easy, hard, already code in someone's directory?

Also, does anyone have a preferred method of converting standard
deviations (of x randomized sequence comparisons, as done in GAP/RAND)
to probabilities that gapped alignment of two sequences yields a
quality by chance?

Thanks

Arle
*************************************************
a.k.a. Dr. Arthur L. Kruckeberg
Department of Biochemistry and Molecular Biology
University of Leeds
Leeds LS2 9JT
Great Britain
+44 532 333172
+44 532 333167 FAX
arle at biovax.leeds.ac.uk
*************************************************



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