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&...
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P.S. BLASTZ is considered obsolete, and has been replaced by LASTZ.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