Needleman-Wunsch - producing more than the optimal solution -- pleasehelp

[almurph@altavista.com]

Folks,

I want to modify the Needleman Wunsch algorithm (pseudo-code here:
http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm) so that it
produces more than the optimal solution.

What I want is the optimal solution, second optimal solution, third
and so on do the chain.

Problem is though I don't know how to do this. Can anyone help
please? Any comments/suggestions/code-sample would be most
appreciated.

Thanks,
Al.

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RE: Needleman-Wunsch - producing more than the optimal solution -- ple

Hi Chris,
I am not sure exactly what you have right now, but I have been using a
Smith Waterman alignment algorithm I got from SourceForge
(http://jaligner.sourceforge.net/naligner/) which seems to work pretty well.
I have thought about trying to get it to do pretty much what you have said
you are looking for, but have not yet done so. If it would be helpful,
perhaps we could work on this together? I never have quite wrapped my brain
around these dynamic programming algorithms and perhaps it is time.
Let me know if you are interested.
Ethan

Ethan Strauss Ph.D.
Bioinformatics Scientist
Promega Corporation
2800 Woods Hollow Rd.
Madison, WI 53711
608-274-4330
800-356-9526
ethan.strauss@p romega.com


"almurph@altavi sta.com" wrote:

Folks,
>
I want to modify the Needleman Wunsch algorithm (pseudo-code here:
http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm) so that it
produces more than the optimal solution.
>
What I want is the optimal solution, second optimal solution, third
and so on do the chain.
>
Problem is though I don't know how to do this. Can anyone help
please? Any comments/suggestions/code-sample would be most
appreciated.
>
Thanks,
Al.
>