[BiO BB] Testing a smith-waterman algorithm?

[Theodore H. Smith]

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:

> Hi
> 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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