[Genome] protein to dna blat / protein to genome blat alignment

Finney, Richard (NIH/NCI) [E] finneyr at mail.nih.gov
Mon Dec 10 10:20:31 PST 2007


Is there a way to get command line blat to do protein to dna (protein to
genome) sequence alignment? I get the message "d and q must both be
either protein or dna" when running a command like this 

"blat -t=prot =q=dna chr1.fa p.fsa output.psl" 

Normally, I'd take the error message at face value, but I'm a little
stumped
because the hgBlat server does do protein to genome alignment.

I've probably annoyed your sysadmins before by setting up curl/wget
scripts to torture your servers to get this information but would really
like to do
it locally via command line.

Thanks for any thoughts and help on this.





More information about the Genome mailing list