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Old 12-18-2014, 11:31 AM   #1
JenBarb
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Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47
Default 16S gene genomic coordinates?

Hello,
I have a couple of questions.

Does anyone know where I can get the true genomic coordinates of the 9 different variable regions in the 16S gene?
I have these based on my own inference from some published figures of the gene but would like to know if they are correct:
V1 ~ 80-120
V2 ~ 170-200
V3 ~ 420-500
V4 ~ 610-700
V5 ~ 820-950
V6 ~ 960-1100
V7 ~ 1150-1200
V8 ~ 1220-1300
V9 ~ 1450-1500

Also, does anyone know if there is a tool that I could use where I could blast roughly 100K reads against a database of bacteria and get back the region where my sequences aligned?

thank you,
Jen
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