On Thursday, August 30, 2012 3:46:48 PM UTC-4, Dakota wrote:
This is pretty neat, if I remember you are the one that payed to get the Neurospora genome sequenced for your own data?How did you go about chosing these 1014 bps for your synthetic promoter? I imagine there are multiple promoter sequences, what about an entirely new one?I was just messing around looking at the H1 gene, but I get so lost in genome software and usually quit from frustration. I just want to see the ssDNA sequence upstream and downstream of that gene but can't figure out how.Out of curiosity, why are those repeat homopolymers needed? The cytosine run of 11 bp's in the already rich GC area seems to be something they had trouble with.Unfortunately I do not have experience with this to offer any help, but it is a pretty sweet project!
I just picked that sequence since somebody else had used it in a construct as a promoter and it was sufficient to drive expression, cant remember the reference offhand. I dont know why those repeats are needed, or if any detailed promoter bashing of this sequence has been done, likely not. Why they are there? Either they are needed or an evolutionary accident I suppose.
The Broad display of this genome is a bit clunky, but I find it easier to use that the version at Ensembl Genomes, and the UCSC Browser people do not do much support of micro-organisms.
Funny you should ask about the genome, I just put up the current status of that project in a different post, the link is below.
http://www.roningenetics.org/Sequencing.html
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