Protocol Online logo
Top : Forum Archives: : DNA Methylation, Histone and Chromatin Study

Bisulfit treated DNA sequence analysis - (Sep/27/2005 )

Hi, Nick

Is there any software that can help in sequence analysis sequence after the bissulfit treatment?

And a silly question, why some people clone the sequence into a vector and pick 10-14 clones to sequence? If there are some C unconverted, then how to identify these sites are pseudo-methylated sites?


hi mou1

there aren't many software packages available to do just that, I have had to hand draw the results with coraldraw or illustrator.

there is a program I did come across very early on in my project called methtools MethTools and can be found here.

cloning and sequencing 10-14 clones will give you the methylation pattern of selected amplicons within the population of your template DNA. The more you seqeunce the more representative the pattern will be to the population. Pseudomethylated sites i assume are sites which are partially methylated? if so, there will be clones that you seqeunce where at a particular CpG site is methylated © while in other clones that same CpG site is unmethylated (T).

good luck!!