Genome-wide CpG island finder

Question

[Satyajeet Khare]

Hi Biostars,

I am looking for a tool for finding CpG islands in a draft genome-assembly. I see some tools which are web-based with input limit. I also see some tools that are specialised for mammalian genome promoters. The organism is non-mammalian. Some tools use epigenetic marks. I don't have DNA methylation data.

Is there a tool or a script that can use large FASTA files and find CpG islands?

Answer 1

[lakhujanivijay]

Hi Satya,

Have you already tried cpgplot, available here?

[Satyajeet Khare]

Looks like I will have to play with parameters as the draft genome is AT rich.

Thanks.