Mutate protein sequence according to HGVS

Question

[dariober]

Hi- Before I reinvent the wheel... I need to modify a set of reference protein sequences in fasta format according to given variants in HGVS format.

Can you suggest any tool or package to do it? A Python package would be best but any would do (R, Java, standalone...). The hgvs package seems promising but from a quick glance I'm not sure it can do it...

Example: given sequence

>ENSP00000454338
FPIEAGDSRGLAAAPESQDSPEAVATEHNPVSGPCRASISPGRFVAALDATA

And variant:

ENSP00000454338.1:p.Ala37Thr

Return the input with Ala at position 37 changed to Thr:

>ENSP00000454338
FPIEAGDSRGLAAAPESQDSPEAVATEHNPVSGPCRTSISPGRFVAALDATA

This should be easy to code for most cases but some may be tricky, e.g. Met178ArgfsTer153

[Ram]

It does seem weird that they don't have it already, but it should be pretty straightforward (I think) to code using their package. I'd recommend getting c. from the p. and making a change in the cDNA sequence for all changes where posedit.length > 1 (indels, fs, etc).

Answer 1

[Emily]

There's a Protein Sequence plugin for the Ensembl VEP. Run the VEP with HGVS input and this plugin to get the sequences in your output. It's open source, so you can borrow the code and do it your own way too.