On Nov 25, 2010, at 9:20 AM, pande wrote:
Can you please enlighten me on the concept of MAF alignments ? Are they the same as BLASTZ searches ????
The short answer is that MAF is just a file format for reporting local alignments of 2 or more sequences: http://genome.ucsc.edu/FAQ/FAQformat#format5
A longer answer is that MAF is the format by which UCSC reports their many-species alignments, such as the 46-species alignment referred to here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=157689212&c=chr21&g=c...
BLASTZ doesn't produce MAF as output, and it is only a pairwise aligner. However, it is (actually, was) a piece of the MULTIZ package which combines pairwise alignments into a multiple alignment and does produce MAF.
Hope that helps, Bob H
P.S. BLASTZ is considered obsolete, and has been replaced by LASTZ. http://www.bx.psu.edu/miller_lab http://www.bx.psu.edu/~rsharris/lastz