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] > >> > >> _______________________________________________ > >> Bioc-sig-sequencing mailing list > >> [email protected] > >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >> > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > -- > 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] > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
