To Whom It May Concern,

Sorry to bother you with what is likely a fairly simple problem, but I have 
trying to figure this out myself for several days and just can't figure out how 
to do it.

I have a set of 8766 genes that I would like to test for positive selection in 
using various other programs (HyPhy for example). To do this I obviously need 
an alignment of these genes across various species, but I just can't figure out 
how to get the alignment in a fasta format. For example, I have a BED12 file 
from UCSC with the data for the 8766 genes, I thought the easiest way was to 
use the "Stitch Gene blocks" option and then select locally cached alignments 
as the MAF source for the species I care about. However, because these 8766 
genes have multiple transcripts I end up with 23,581 regions. Is there a way to 
merge the multiple regions for each gene into a single region for the longest 
transcript? Then I should have 8766 regions and can use Stitch Gene blocks". 
(Unless there is a more economical way to do this.)\


Vincent J. Lynch, Associate Research Scientist
Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute
Yale University
"There is a grandeur in this view of life, with its several powers,
having been originally breathed into a few forms or into one; and that
whilst this planet has gone on cycling according to the fixed laws of
gravity, from so simple a beginning endless forms most beautiful and most
wonderful have been, and are being, evolved." -C. Darwin, 1859

(Walker, Wisconsin, Madison, Maddow, Tea Party, Obama, global warming)

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