Question: Genome-wide CpG island finder
1
gravatar for Satyajeet Khare
2.1 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k wrote:

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?

genome • 1.5k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 2.1 years ago by Satyajeet Khare1.5k
2
gravatar for lakhujanivijay
2.1 years ago by
lakhujanivijay4.6k
India
lakhujanivijay4.6k wrote:

Hi Satya,

Have you already tried cpgplot, available here?

ADD COMMENTlink written 2.1 years ago by lakhujanivijay4.6k

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

Thanks.

ADD REPLYlink written 2.1 years ago by Satyajeet Khare1.5k
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