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.)\


Thanks
Vinny




Vincent J. Lynch, Associate Research Scientist
Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute
Yale University
http://pantheon.yale.edu/~vjl4/profpage/
 
"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)







___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to