[Biojava-l] SW and NW

[Thomas Down]

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.