Consensus sequence

Dan Davison davison at UHNIX2.UH.EDU
Mon Jan 22 18:17:01 EST 1990


> 
> Does anyone know of a program that will align many DNA sequences, and
> determine a consensus sequence? Or maybe a program that will take an
> alignment of sequences and than determine a consensus?
> Preferably a public domain program.


Mike Waterman has a program, RALIGN, which does consensus multiple
sequence alignment.  A reference is Mathematical Methods for DNA
Sequences, Ed. M. Waterman, CRC Press, 1989, Chapter 3, "Sequence
Alignments", by M.Waterman, pp53-92; 81-92 is some C code for the
basic algorithm, without drivers.

Dave Lipman's group has recently published a paper in PNAS USA, 1989,
on their program MSA, Multiple Sequence Alignment.

Both programs have been available in the past from the authors.

dan

-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77054-5500/davison at uh.edu/DAVISON at UHOU

"Mars is essentially in the same orbit...somewhat the same distance
from the sun, which is very important.  We have seen pictures where
there are canals, we believe, and water.  If there is water, that
means there is oxygen.  If oxygen, that means we can breathe" -- Vice
President Dan Quayle, Head of the National Space Council, when
questioned on CNN about why America should send a mission to Mars.
[Houston Post, Sun. Nov. 19, pg. C-1].

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.






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