[Genome] Chimp assembly 2 pairwise alignments

[Daniel Gaffney]

Hi there,
I have ~ 1500 small regions in the human genome, for which I would like 
to get the human-chimp
pairwise alignment for the latest chimp assembly. However, I'm having a 
little trouble in figuring out the best
way to do this - can this be done locally? Or is there a batch 
submission tool that I can retrieve all alignments
from UCSC directly - I've tried the table browser, but I can't seem to 
get the specific region I want (i.e. if i select the chimp chain
track, and retrieve sequence, I get the the alignment of that entire 
region, not just the region corresponding to the coordinates I've
entered). Any ideas?
Cheers
Dan

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Daniel Gaffney		          

McGill University and Genome Quebec Innovation Centre
740 ave Dr Penfield Rm 7208
Montreal (Quebec)
H3A 1A4

http://dutch.cap.ed.ac.uk/

Tel: +1 514 398 3311 ext: 04592
Fax: +1 514 398 1790
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