Thomas and Lana,
The pairwiseAlignment() function supports vectorized alignments where
either a vector of sequences can either be aligned to a single sequence
or to a vector of sequences where pattern[1] is aligned to subject[1],
pattern[2] is aligned to subject[2], etc. The looping is then pushed
down to the C level, which is much faster than looping at the R level.
Patrick
Thomas Girke wrote:
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
[email protected]
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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
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
[email protected]
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