[Bioc-sig-seq] gapped alignment

[Lana Schaffer]

Hi,
I would like advise about how to do gapped alignment
with output from Solexa sequencing.  We have a new
virus and would like to know homology to known
polymerase sequences.  Does someone know if MAQ
would be a good program for this purpose using
gapped alignment?  Or would it be best to do
De Novo alignment and then use Blast?
Thanks for any advise. 

Lana Schaffer
Biostatistics/Informatics
The Scripps Research Institute
DNA Array Core Facility
La Jolla, CA 92037
(858) 784-2263
(858) 784-2994
schaffer at scripps.edu