Hi, Medha! See answers below.
-Galt 7/12/2011 9:14 AM, Bhagwat, Medha (NIH/OD/ORS) [E]: > I am trying to understand BLAT query type provided on the web: > > DNA, protein, translated DNA and translated DNA and Blat's guess. > > 1. DNA: input DNA sequence will be searched against DNA database Yes. The query will be searched against the dna database positive strand. Then the query is reverse-complemented, and the search is run again. Note that this is mathematically equivalent to having searched the negative strand with the un-reverse-comlemented query. For protein and translated BLAT, both the positive and negative strands (in all 3 frames of each strand) of the dna database are indexed and searched. > 2. protein: input amino acid sequence will be searched against translated DNA > database Searches the protein query against 6 frames of translated database. > 3. translated DNA: input DNA sequence. BLAT will translate the input DNA > sequence in all 6 reading frames and compare to the 6 frame translated DNA > database > (user does not provide translation but provides DNA). BLAT will translate the DNA query in 6 reading frames and then search the dna database translated in 6 frames. (One would not do this unless uncertain about whether the query sequence was from the active strand or not, as is the case for some ESTs for example.) > 4. translated RNA: input DNA sequence. BLAT will translate the DNA query in > 3 reading frames on one strand and compare to the 3 frame translated DNA > database.(again, user does not provide translation but provides DNA) > BLAT will translate the DNA query in 3 reading frames and for each one will then search the dna database translated in 6 frames. > Is this correct? > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
