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Old 05-19-2014, 04:44 AM   #1
Noa
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Location: haifa israel

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Default comparing CpG islands between species

Hi all,
We are considering using chips developed for human CpG island detection for non model organism methylation analyses
Does anyone have useful insights into how best to compare CpG islands between organisms to see whether this would make any sense? I worry that it wont just be a simple blast... but cant seem to find any literature on this or relevant tools at all
Thanks
Noa
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Old 05-19-2014, 12:22 PM   #2
dpryan
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How complete is the genome of your organism? If you have a good idea of the sequence then you could at least blast the primers from the human array and see how distant they are.
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Old 05-19-2014, 10:29 PM   #3
Noa
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The genome is in scaffolds but reasonably complete. I am not sure whether blast will be sensitive enough given the CG richness of the islands etc. Happy if anyone has any previous experience with this (or a gut feeling on whether blast is the way to go with this one).
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