[Biojava-l] DNA: Many to one alignments

[Jeremy Lewi]

HI biojava users,

I'd like to align N DNA sequences to my reference sequence. I don't know
which strand of my N query sequences will be the best match for my query
sequence.

Right, now I do this by doing 2N pairwise alignments where I separately
align each query and its reverse complement to the reference.

Is there an easier, more efficient way to do this and build the alignment
profile for my N sequences to the reference?

Thanks
J