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 _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user