[BiO BB] Testing a smith-waterman algorithm?
Theodore H. Smith
delete at elfdata.com
Sat Mar 11 14:20:21 EST 2006
A suffix tree is not suite to doing the kind of protein matching I
will be doing, though. I'm not doing English, I'm doing proteins. I
just used English examples because it's easier to understand.
On 11 Mar 2006, at 16:32, Kalidas Yeturu wrote:
> 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
> A local alignment should be able to figure out that "establishment"
> aligns well in this case.
> Is that basically how Smith-Waterman helps us?
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