4 replies to this topic

[Samantha]

I would like to predict whether the 5'region of a gene contains CpG islands..I pasted the ~10000nucleotide from the last nucleotide of the exon 1 to CpG island searcher . is it enough? should i include intron 1 and exon 2?


samantha

[methylnick]

sounds good samantha, though it wouldn't hurt to included intron 1 and exon 2 as the island of some genes run into these regions.

Good luck!

Nick

[Samantha]

Then how long of the 5'region do you guys usually use for CpG island prediction? and which regions do you usually use, or is there a common rule for the prediction, say we have to use intron 1+ exon 1+ exon 2 for prediction? Thanks

samantha

Edited by Samantha, 23 March 2005 - 06:49 PM.

[pcrman]

For methylation study, I only focus on the cpg islands that surround the transcriptional start site unless there are identified transcriptional regulatory elements further upstream.

[pcrboy]

One trick I sometimes use is to paste those 10kbp onto microsoft word, then highlight all possible CG (very quick). That gives yourself a nice visual of where CpG islands may be located.