[Biojava-l] IndexOutOfBounds Exception when performing Pairwise Alignment

[Andreas Prlic]

Hi Hannes,

Couple of things in response to your mails:

- thanks for providing the example, I have moved it to  a Cookbook
page, since we had several DNA alignment related questions recently.
http://biojava.org/wiki/BioJava;CookBook3:PSA_DNA

- I believe the AmbiguityDNACompoundSet is required, to match the
compound set of the substitution matrix.

-   about your sequence matching strategy: this really depends on your
size and similarity of DNA sequences. if you have many, then blast
might be the way to go, otherwise just looking a number of identical
positions (psa.getNumIdenticals())  might be a quick and dirty
solution for this as well.

- ConcurrencyTool is just a utility class for working with the Java
concurrency framework. Should be easy to write your own Callable
classes that do pairwise alignment, if you needs to do this in
multiple threads...

Andreas