Hello Louis, You are correct that tBlastX returns amino acid alignments. With BLAT, while the comparison also performed between at the protein level, the BLAT result the nucleotide alignment.
More detail: Translated RNA - 3 frame translation (stranded) Translated DBA - 6 frame translation (no strand info) Hopefully this is helpful. The BLAT documentation may also be useful: BLAT help: http://genome.ucsc.edu/FAQ/FAQblat.html http://genome.ucsc.edu/goldenPath/help/blatSpec.html Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/15/10 8:52 PM, louis wrote: > Hi, > > I am confused by the BLAT option "translated DNA"& "translated RNA" > > Originally I expected BLAT behaviored as follows: > > Query Type: > DNA: search a nucleotide database using a nucleotide query > Protein: Search a translated DNA database using a protein query > Translated DNA: Search a translated DNA database > using a translated DNA query > Translated RNA: Search a translated DNA database using > a translated RNA query > > Therefore, I expected the translated DNA& translated RNA result > representation was similar to that of tblastx > > However, this assumption seems to fail and the side-by-side alignment > shows only DNA match/mismatch. > > So what does translated DNA/RNA really mean in the BLAT context? > > > Cheers, > > > Louis > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
