Detected Variants' Effect on Primary Structure of a Protein (Arabidopsis)

Question

[shanika.amarasinghe]

Hi,

I'm a student who is new to this aspect of bioinformatics in my work. I deeply apologize if this is a silly question. But I'm stuck at the point where the analysis for the variants are done. I see that lots of work are done for human genome. But I want to analyze variants from Arabidopsis.

What I have done so far : identified and extracted the SNPs (in vcf format) from accessions for Arabidopsis for a protein coding gene

What I want to do: Map those back in to a reference gene/or genome (I have both) I have downloaded and convert it to an amino acid sequence to see whether the nucleotide polymorphism has an effect on the amino acid sequence

Can you please help? Thanks a lot.

Answer 1

[Ram]

One of the tools I'd recommend for this is snpEff

It is a software package that predicts the effects of SNPs, especially their effects on protein coding and splicing. I have seen it do great with human data, but I think as long as you have a reference sequence, there should not be a problem, ideally.

If you have access to a Galaxy server or a local cluster, you could check out if it has snpEff integrated/installed in it.

EDIT: I just checked, the following Arabidopsis databases are available for snpEff to work with:

alyrata1                               Arabidopsis_lyrata
alyrata107                             Arabidopsis_lyrata
athaliana130                           Arabidopsis_Thaliana
athalianaTair10                        Arabidopsis_Thaliana
athalianaTair9                         Arabidopsis_Thaliana
v.1.0.21                               Arabidopsis_lyrata

Answer 2

[Emily]

You can run the Variant Effect Predictor on them.