all internal repeats with mutation

CSHL wli at phage.cshl.org
Wed May 19 14:31:26 EST 1993



thanks for all the postings explaining the finding-all-internal-
repeats method. so now i know  that in principle, it is a trivial 
problem (solution: overlapping all its suffix, or, sorting all 
suffix).

as a follow up question, what about (1) finding all internal
repeats with at most one mutation?  (2) finding all internal
repeats with at most a fixed percentage mutation rate (say,
1 out of 6)? the difference between (1) and (2) is simply
that in (2) one can allow more number of mutations for
repeats of longer size. 

i can see that in the "sorting of all suffix method",
if the mutation occurs at the first site of the suffix,
it's going to be a problem. it seems OK if the mutation
occurs in other sites. what's the solution to this? again,
apology if it's a trivial question....

w.li, CSHL, wli at cshl.org




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