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 ? _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
