Re: [galaxy-user] This thing called MAF
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 ????
and on Nov 25, 2010, at 9:33 AM, Bob Harris replied:
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
[[ more, snipped ]]
It turns out there's another format with the same name, MAF, as part
of the MIRA sequence assembler project. This is completely unrelated
to UCSC MAF. See
http://mira-assembler.sourceforge.net/docs/chap_maf_part.html
Looking at that description it seems to fit the general idea of SAM,
i.e. it's a short-read-focused format that allows a read mapper to
convey information to an assembler.
Now, I'm sure the original poster was asking about UCSC MAF, not MIRA
MAF, but the galaxy team should be aware that there are two different
things called MAF in this field.
Bob H