Question: Detected Variants' Effect on Primary Structure of a Protein (Arabidopsis)
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gravatar for shanika.amarasinghe
6.2 years ago by
Australia
shanika.amarasinghe30 wrote:

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.

 

snp arabidopsis genome • 1.5k views
ADD COMMENTlink modified 6.1 years ago by Emily_Ensembl21k • written 6.2 years ago by shanika.amarasinghe30
2
gravatar for _r_am
6.1 years ago by
_r_am30k
Baylor College of Medicine, Houston, TX
_r_am30k wrote:

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
ADD COMMENTlink modified 13 months ago • written 6.1 years ago by _r_am30k
1
gravatar for Emily_Ensembl
6.1 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

You can run the Variant Effect Predictor on them.

ADD COMMENTlink written 6.1 years ago by Emily_Ensembl21k
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