Argh ... I had already shut down my laptop when I understood what you mean ... well too late to update! :)

Anyway when using C, my approach to start with the longest is for sure better and one can avoid allocation problems.

But I'm sure there are already much more efficient algorithms out there (something like presorting the input in a dynamic tree) and there is no need to reinvent the wheel.

And analyzing sequences is such a common task in bioinformatics, that I can hardly imagine that none of the BioPerl modules already include necessary routines. (just 50% inclusion redundancy is IMHO a very low estimation)

Thats very likely an xy question, because normally the next step is to find overlapping endings to reconstruct the original DNA.

Cheers Rolf

In reply to Re^18: list of unique strings, also eliminating matching substrings by LanX
in thread list of unique strings, also eliminating matching substrings by lindsay_grey

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