It looks like the command line tool we have for this expects the mafs to be loaded into a UCSC style database. I have a feeling that the galaxy tools that James Taylor mentions will be easier to use in your context.
On Jan 23, 2009, at 5:28 AM, Abhi Ratnakumar wrote:
Hello,
I have multiple sequence alignment files in the *maf format, containing whole genome alignments from 6 species. I'm interested in extracting the sequence surrounding the exons of ~16,000 genes. I was wondering if it would be possible to run the Alignment Extractors tool in batch? Would it be possible for me to run it on the command line?
Thanks ins Advance Abhi Ratnakumar
By the way I'm a PhD student at Uppsala University, so any executables that you provide will be used for academic purposes only.