Question: Approximate Sequence Matching Libraries For The Jvm?
3
gravatar for Gabriel Mitchell
7.3 years ago by
Atlanta
Gabriel Mitchell530 wrote:

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.

alignment java sequence • 926 views
ADD COMMENTlink modified 5.8 years ago by Audriusa10 • written 7.3 years ago by Gabriel Mitchell530
2
gravatar for Pierre Lindenbaum
7.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum100k wrote:

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

ADD COMMENTlink written 7.3 years ago by Pierre Lindenbaum100k

There it is! Thanks.

ADD REPLYlink written 7.3 years ago by Gabriel Mitchell530
0
gravatar for Audriusa
5.8 years ago by
Audriusa10
Switzerland
Audriusa10 wrote:

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.

ADD COMMENTlink written 5.8 years ago by Audriusa10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1446 users visited in the last hour