Question: Genome-wide CpG island finder
0
gravatar for Satyajeet Khare
19 months ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k 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 • 1.2k views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 19 months ago by Satyajeet Khare1.3k
2
gravatar for Vijay Lakhujani
19 months ago by
Vijay Lakhujani4.1k
India
Vijay Lakhujani4.1k wrote:

Hi Satya,

Have you already tried cpgplot, available here?

ADD COMMENTlink written 19 months ago by Vijay Lakhujani4.1k

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

Thanks.

ADD REPLYlink written 19 months ago by Satyajeet Khare1.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 736 users visited in the last hour