Question: How to predict the effect of DNA base deletion on protein?
0
gravatar for abc.faisal
8 months ago by
abc.faisal0
abc.faisal0 wrote:

I was wondering if any tool is available to predict the effect of DNA base deletion at protein level?

I would like to explore the consequences of deletion mutation.

snp gene • 432 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by abc.faisal0

VEP and SnpEff are good if you want a command-line tool to integrate into your pipeline. If you want to further investigate the consequences of just a couple of variants, you can try for example PredictSNP2, Consurf, ProtScale and Protter.

ADD REPLYlink written 8 months ago by pristanna520

Or VEP online

ADD REPLYlink written 8 months ago by Emily_Ensembl18k

I was thinking to translate DNA sequence (without deletion and with deletion) into protein sequence and compare them using the tools you mentioned. Does this make sense to you?

ADD REPLYlink modified 8 months ago • written 8 months ago by abc.faisal0
3
gravatar for finswimmer
8 months ago by
finswimmer11k
Germany
finswimmer11k wrote:
ADD COMMENTlink written 8 months ago by finswimmer11k

I have already found a deletion of C at SNP (8:21984668 C / A). How can I predict deleterious impact of the deletions at protein level?

ADD REPLYlink written 8 months ago by abc.faisal0

You run it through the tools that Fin mentioned.

ADD REPLYlink written 8 months ago by Emily_Ensembl18k
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