CpG Island prediction
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4.9 years ago
mittu1602 ▴ 180

I have a nucleotide sequence fasta file which is more than 20mb size and I am looking for tools that predict/site cpg islands with the reference genome I have and not Human genome. I have tried tools like cpgplot, newcpgreport, CgiHunter and more CpG tools list

but almost all support human reference genome or cannot except files more than 10mb files. Any other way to find CpGs or any other tools?

Thank you.

cpg genomics • 3.1k views
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I do not have an overview over the field and therefore cannot add much but would suggest not to look at omictools.com. Their list is almost certainly incomplete and outdated like in this case where the three tools labelled "new" (including newcpgreport and cpgplot) are from 1999, 1999 and 1992! That's not even old anymore in bioinformatics terms (not implying that its bad).

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Thank you for the suggestion, I'll have a look on it

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I don't know if you're still looking for an answer to this, but I've found some success with CpGcluster 1.0. It also doesn't have any of the constraints you've mentioned here iirc.

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