Finding Non-Synonymous Mutations

Question

[Matt]

Does anyone know of existing Python code that given a nucleotide substitution will tell you whether or not that mutation is synonymous/non-synonymous? Ideally, I would give this function a GFF file along with the substitutions(s) and it would give me back the amino acid changes, but I'll take anything that's sort of along these lines. Also, I realize this is relatively straightforward to code myself, but I figured I'd ask before I reinvented the wheel. Thanks in advance.

-Matt

[Michael Schubert]

Have you looked at BioPython? This should be somewhere close to a 1-liner.

[Matt]

My first thought about this problem exactly. I'm not a BioPython expert, but after digging around the tutorial, manual, and googling, I couldn't find anything.

[Michael Schubert]

I overread the GFF part. This would be more complicated as it is currently not supported natively (as Brad told me today).

Answer 1

[Matt]

Finally found this program:

http://snpeff.sourceforge.net/

Granted, it's not a Python module/function as specified in the question, but it will suit my needs as it'll be easier to run this through my current Python script and simply parse the output than to actually implement the mutation classification. Would be nicer to have a completely python solution if anyone knows of any, but in case anyone else runs into this issue, hope this link helps.

Answer 2

[Dede]

Did you figure out how to know the synonymous vs nonsynonymous from vcf/gff files? I really want to know how?