Question: Extract Alignment For A Set Of Genes
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Vincent Joseph Lynch • 40 wrote:
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)
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modified 7.5 years ago
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Jennifer Hillman Jackson ♦ 25k
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7.5 years ago by
Vincent Joseph Lynch • 40
