Question: How to locate the intergeneic SNPs in cis-regulatory element
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gravatar for gzr3150
3.6 years ago by
gzr31500
China
gzr31500 wrote:

Hi, I am a beginner in genome field and I hope some teachers can give me a guidence.

Now, for example, I have some SNPs in a whole novel genome, and I have genome sequence (fasta) and SNP resequencing data. I want to know whether they are in cis-regulatory element or not ? Do anyone know what softwares or approaches can do this ? Or are there any softwares can predict the cis-regulatory element position from a novel genome sequence (fasta) ? Thanks a lot.

snp genome • 1.0k views
ADD COMMENTlink modified 3.6 years ago by vassialk190 • written 3.6 years ago by gzr31500
0
gravatar for vassialk
3.6 years ago by
vassialk190
Belarus
vassialk190 wrote:

Try NextGene and MAUVE software and do alignment with variant calls, if I understand correctly what you want and need...

ADD COMMENTlink written 3.6 years ago by vassialk190

Thanks vassialk, I have not used this two softwares. Maybe I did not convey my question clearly. Now, I have finished SNP calling, so I know the SNP position in my genome. And I want to know how many SNPs are in cis-regulatory element. My idea is that I can predict the cis-regulatory element of my whole genome, but I don't know whether are there this softwares. The second idea is about ENCODE databases, but I know a little about ENCODE.

ADD REPLYlink written 3.6 years ago by gzr31500
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