How to predict the effect of DNA base deletion on protein?

Question

[abc.faisal]

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.

[pristanna]

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.

[Emily]

Or VEP online

[abc.faisal]

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?

Answer 1

[finswimmer]

• VEP
• SnpEff

[abc.faisal]

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?

[Emily]

You run it through the tools that Fin mentioned.