[Bioc-sig-seq] gapped alignment

[Thomas Girke]

That's true. The Smith-Waterman alignment algorithm implemented in Biosting's
pairwiseAlignment() will give even higher sensitivity then BLAST. To use it
as a search tool, one would simply loop over the database sequences. 

Thomas

On Fri, Apr 24, 2009 at 10:54:48AM -0700, Robert Gentleman wrote:
> given that it is short, why not use the pairwiseAlignment tool in Biostrings,
> which would allow you to use gaps +/- quality scores etc?
> 
> 
> 
> Thomas Girke wrote:
> > 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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> >> Bioc-sig-sequencing at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>
> > 
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> > 
> 
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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> rgentlem at fhcrc.org
>