[Biojava-dev] Integer aligner

[Richard Holland]

Hello.

Take a look at: http://www.biojava.org/wiki/BioJava:CookBook:DP:PairWise2

Then, you can develop your own file to feed into SubstitutionMatrix to
inform the algorithm as to how to match up the symbols in the alphabet you
are using. Use that file in combination with an instance of your own Integer
alphabet, and you should find the rest of it works fine.

cheers,
Richard

PS. The substition matrix file format should follow the format of the files
at ftp://ftp.ncbi.nlm.nih.gov/blast/matrices

2008/9/8 Klérisson Paixão <klerissonpaixao at gmail.com>

> Hey everyone!I really need to align integers. My alphabet won't be DNA, nor
> RNA, neither Protein. It must be integers, numbers.
> How can I do it using biojava?
> Thanks a lot!
> Klerisson
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-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/