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Finding maximally divergent segments

Olav Hungnes olav.hungnes at labmed.uio.no
Fri May 7 19:15:34 EST 1999

I'd guess that GCG's PlotSimilarity would give you an answer:

PlotSimilarity calculates the average similarity among all members of
a group of aligned sequences at each position in the alignment, using
a user-specified sliding window of comparison. The window of
comparison is moved along all sequences, one position at a time, and
the average similarity over the entire window is plotted at the middle
position of the window. The average similarity across the entire
alignment is plotted as a dotted line. 


On 4 May 1999 12:27:12 -0700, s b <biolinux at yahoo.com> wrote:

>Hi all,
>I'm wondering if there is any software or algorithms, given a set of
>DNA sequences  to find a maximally divergent segment (of length N) in
>each sequence so when aligned to all other sequences it is of the
>highest divergence.  Most people are looking for similiarities but I'd
>like to do this!!  I guess that I could use blast, but that would give
>me similarities.  I tried flipping scores for matches and mismatches
>but it did  not quite work!!
>Do You Yahoo!?
>Get your free @yahoo.com address at http://mail.yahoo.com

Olav Hungnes                                  olav.hungnes at labmed.uio.no
Natl.Inst.of Public Health, Dept.of Virology  olav.hungnes at embnet.uio.no
P.O.Box 4404 Torshov,                          phone: (+47)22 04 25 20
N-0403 OSLO, NORWAY                            FAX:   (+47)22 04 24 47

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