This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Finding Non-Synonymous Mutations

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

python mutation non
• 8,218 views • link
updated by Dede • Dede • written by Matt • Matt

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

• 0 views • link
written by Michael Schubert Michael Schubert

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.

• 0 views • link
written by Matt • Matt

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

• 0 views • link
written by Michael Schubert Michael Schubert

2 answers

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.

• 1 views • link
written by Matt • Matt

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

• 0 views • link
written by Dede • Dede

Log in to answer this question.

More posts like this