sequence variant notation and formatting

Question

[kevin.stachelek]

I am trying to connect a database of sequence variants with information on dna and protein level changes to a tool that plots lollipop plots of those same variants. The database seems to use one protein variant notation and the plotting tool another. I would like to translate between the two, but don't know the formal rules of either notation, nor where to look them up. examples of each notation are listed below. I would also appreciate an automated tool that can handle this translation preferably via R/bioconductor

database: p.S4F

plotting tool: L858R

Answer 1

[Ram]

Please read: https://varnomen.hgvs.org/

It has all the information you need. As for your examples, the only difference is that one has the p. prefix while the other doesn;'t (which it should).

[kevin.stachelek]

Thank you

It is good to know that the first format is in accordance with HGVS Sequence variant nomenclature and that the second is a simplification. For reference I am using MutationMapper which relies on the simplified format which I am adapting for COSMIC data by just truncating the preliminary 'p.'