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
