Re: Biojava-l Digest, Vol 99, Issue 12

Consider Kalirin , a multidomain protein.

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=NP_003938.1

Now, lets say I aligned Kalirin with a single domain member of the RHO-Gef
family....  Then only one part of the sequence would match....  But what if
I WANTED a global alignment, for programmatic purposes... Then I would want
an alignment like this

------------------------------------------------RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF------

With lots of gaps in the beggining, and lots of matches at the end, where
the length of the alignment between the two proteins was exactly equivalent.
 Contrast this with a smith waterman output, which would look like this :

RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF....

So is there a way to get the specificity of Smith Waterman in a Needlman
Wunsch alignment ?
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