Approximate Sequence Matching Libraries For The Jvm?

Question

[Gabriel Mitchell]

I am currently working on some toy problems to teach myself about sequence alignment. I want to benchmark my efforts against the performance of existing libraries for the JVM (I am developing in Clojure right now). I have learned that org.apache.commons.lang.StringUtils implements Levenshtein distance between two string. However, I will eventually be interested in the problem where different mutations are weighted differently (i.e. insertion may have a higher penalty than substitutions). Can someone point me to a mature Java or Jython library that does this ? I am NOT talking about BLAST or other heuristic methods. For now I want to benchmark against exact methods.

Answer 1

[Pierre Lindenbaum]

I just found this one in my delicious bookmarks : http://jaligner.sourceforge.net

[Gabriel Mitchell]

There it is! Thanks.

Answer 2

[Audriusa]

Check Sequence_alignment at Ultrastudio.org. The source code under GPL is here. This project also contains several demo applets for various sequence algorithms, also with source code available.