Question: Work with protein sequence in snpeff?
gravatar for olivier.rousseau.1
2.0 years ago by
olivier.rousseau.10 wrote:


I am knew to bioinformatics and I would like to know if it is possible to run the snpeff on protein sequence? I have successfully identified the variant by nucleotide position, but i want to know the codon for each of my sequences. My goal is to identify residue mutation at specific positions. For example, i obtained these results:

nucleotide position | reference | alternative | mutation

226 C T,A p.Leu76Phe p.Leu76Ile

227 T G,C p.Leu76Arg p.Leu76Pro

228 T A p.Leu76Leu

The problem is that it gives me all the possible residues but the codon may not be found in my real aligned sequences. Can i extract the codon for each of the sequences to have residue information? Also can i extract the frequency of each codon in all my sequences per position?

Thank you

Olivier .

ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.0 years ago by olivier.rousseau.10
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The output from SnpEff identifies the position of variation with respect to annotated genes as they map to the reference genome. Use the tool SnpFilter to parse this information. Please see the tool manual for usage details - many of the functions have been implemented in the Galaxy tool wrappers.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson25k
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