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:
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
By the way I'm a PhD student at Uppsala University, so any
executables that you provide will be used for academic purposes only.