[Biojava-l] IndexOutOfBounds Exception when performing Pairwise Alignment

[Andreas Prlic]

> Now, I'm getting null return value - must be still something wrong in
> the parameters...
>
> Where should I start looking for that?

try different gap penalties, I think the default ones are for protein
alignments and one of the blosum matrices...
If that does not help, can you send some of the sequences that are
causing problems? There should be more informative error messages..


> Is there a simple way to align (or score, don't need the full
> alignment) a single DNA sequence against a List of sequences?

You could do a multiple sequence alignment.
http://www.biojava.org/wiki/BioJava:CookBook3:MSA

would it be better to perform a blast search
> (custom "library" to search against) for that?

depends on what you actually want to learn about your sequence. Blast
is good to find matches to new sequences, that you did not know of
before (but has worse alignment quality compared to dynamic
programming).

Andreas