It sounds like you are talking about doing a needleman wunsch alignment, while not penalizing end gaps. This should give you quite similar results to just doing a smith waterman one.
Is it the alignment display that you are concerned about? You could easily fill up the ends with unaligned regions for smith waterman results. I don't find end-gaps particularly informative. Usually an alignment display will give you the aligned positions, then you can easily see (or script) if there are end gaps. Hope that makes sense.. Andreas On Fri, Apr 15, 2011 at 12:30 PM, Jay Vyas <[email protected]> wrote: > 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
