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What programme to use to determine genomic features?


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#1 yoshi

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Posted 21 August 2013 - 12:36 AM

Dear All, my project requires me determine the surronding genomic features (e.g. methylation patterns, DNAse I hypersensitive sites and CpG densities) given different positions in the human genome. In other words, I have a chromosome number and a position on it, and would like to know its surrounding genomic features. Does anyone know of any programmes that I can use to predict the patterns/existence of these genomic features? Thanks in advance.     

 



#2 PhalanxBio

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Posted 21 August 2013 - 08:44 AM

Check out the UCSC Genome Browswer.  I think this will give you the information you need.

 

http://genome.ucsc.e...i-bin/hgGateway



#3 yoshi

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Posted 21 August 2013 - 08:53 AM

Thanks. I've tried that before posting my query here. I thought the output of the analysis is too complicated. For example, when I do not see a methylation pattern around the position in the chromosome of interest, I would like to know how far upstream/downstream from that position would I see a particular methylation pattern. To do this, I zoomed out, and I'm not sure where that position is now on the different tracks of the programme. I've read the userguide, but didn't find it informative enough to use this programme. 






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