[Bioc-sig-seq] gapped alignment

[Thomas Girke]

Dear Lana,

Using a short-read alignment tool in this case will only work, if 
your virus sequences are extremely similar on the DNA level. If that 
is not the case, then you want to use BLAST, PSI-BLAST, SAM, HMMER or 
any other search tool suited for homolog searching. For detecting 
remote homologs for a coding sequence, you definitely want to perform 
the search on the protein level, because it will be much more sensitive.

Short-read alignment tools are optimized for aligning very similar
DNA sequences, but not for finding sequences of low similarity. 

Thomas




On Fri, Apr 24, 2009 at 07:42:21AM -0700, Lana Schaffer wrote:
> 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 
> 
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