[BiO BB] Testing a smith-waterman algorithm?
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
patterns, then SW- helps a lot.
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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