Genome-wide CpG island finder
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3.5 years ago
Satyajeet Khare ★ 1.6k

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 • 2.3k views
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3.5 years ago

Hi Satya,

Have you already tried cpgplot, available here?

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

Thanks.

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