[BiO BB] Testing a smith-waterman algorithm?

Kalidas Yeturu ykalidas at gmail.com
Sat Mar 11 11:32:29 EST 2006

If the task is to set up a query server for finding all common substrings of
length greater than a given threshold, between very very long query
sequences (eg., finding long gene in a very long nucleotide sequence) better
idea would be suffix trees instead of SW-dynamic programming on each query
call. If the sequences are comparitively small and interest is in
analyzing conserved
patterns, then SW- helps a lot.

With Regards
Kalidas. Y

On 3/11/06, Theodore H. Smith <delete at elfdata.com> wrote:
> Hi people,
> I've successfully designed, written and compiled a program that uses
> the smith-waterman algorithm.
> Nothing new there, but it's for an interesting project, and before
> the project is complete, perhaps some questions asked to
> Let's say "disestabishmentarianism" against
> "reestablishmentSomeNonMatchingPart".
> A local alignment should be able to figure out that "establishment"
> aligns well in this case.
> Is that basically how Smith-Waterman helps us?
> --
> http://elfdata.com/plugin/
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