Protein differences in HGVS format

Question

[M. Möller]

I have a bunch of protein sequences (~3.000) that I wish to compare with reference protein sequences, and I want the result in HGVS format. Example:

   ARNDCEQGHILKMFPSTWYV <=> ARNMCEQGHILKMFPSTYV => p.[Asp4Met; Trp18del]

I have written and rewritten routines for this, but with multiple deletions/insertions and/or frameshifts it gets complicated... What are my options?

Thanks.

Answer 1

[Ram]

Oh boy. This is ONE TOUGH task, I'm afraid - it's beyond what most tools are capable of. You might want to check the hgvs python module - if your protein sequence is a known reference protein, you might luck out with their VariantMapper or some such and get the appropriate notation for your mutant protein.

As far as I can see, the module does not support custom alignments, but you might be able to use this module to build your own tool.