Once upon a time, Stephen Montgomery wrote:
> Searching the archives, there was some talk/submissions regarding
> putting in Smith-Waterman in biojava.
> It doesn't look like this ever made it in though.
> I wasn't able to track down where the code may have ended up. (a google
> search shows a SW submission to biojava in august)
I don't recall a submission as such. But Smith-Waterman (and
most other `exhaustive' sequence-alignment algorithms) can be
implemented using pairwise dynamic programming techniques. BioJava has
included a fairly flexible DP toolkit for several years now.
For an example, see the file demos/dp/PairwiseAlignment.java
in the biojava source tree.
Does this sort of thing do what you want?
Thomas.
PS. If you actually want fast, non-exhaustive, sequence
alignment, the experimental org.biojava.bio.program.ssaha
package may be helpful.
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