Promoter sequence - generating phylogenetic tree (Oct/14/2010 )

Hi, I have read many wonderful topics on my question here. Though I still don't understand


I have several genes that I would like to know the promoter sequence of...is Ensemble the place to go?

Then how can I compare the promoter regions? (actual details?)

Is there a way I can tell if my region is methylation sensitive (susceptible is a better word I guess)? Methprimer is a bit weird I thought and I don't believe it cuz i did pyrosequencing and detected some methylation on CpG islands and Methprimer says: no cpg islands found


Thanks
Jassar

>>I have several genes that I would like to know the promoter sequence of...is Ensemble the place to go?

yes, Ensemble provides the best tool for retrieving promoter sequence.

>>Then how can I compare the promoter regions? (actual details?)

What details do you want to know?

>>Is there a way I can tell if my region is methylation sensitive (susceptible is a better word I guess)? Methprimer is a bit weird I thought and I don't believe it cuz i did pyrosequencing and detected some methylation on CpG islands and Methprimer says: no cpg islands found

No. The sequence itself won't tell you there is methylation or not. Methylation and cpg island are two different concept. cpg islands are not always methylated, actually in normal situation, most of them are not methylated.

First all thank you A LOT for replying.

By asking for details I actually meant i have no idea how to do it...

I know that I can get the sequence of the promoter itself, but the format is obviously not accepted in ClustalW. and I don't think puting that sequence in BLAST will be helpful

pcrman on Fri Oct 15 21:15:32 2010 said: