3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures

• DOI: 10.1093/bioinformatics/btae171
• Publication Date: 2024-04-03T00:46:17Z
• Authors: Victoria Ruiz-Serra; Samuel Valentini; Sergi Madroñero; Alfonso Valencia; Eduard Porta-Pardo
• Keywords: 0303 health sciences; Proteins; Genomics; Genòmica; Applications Note; 03 medical and health sciences; Genetic coding variants; Simulació per ordinador; Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica; Mutations in protein-coding regions; 3Dmapper; Software; Biological Specimen Banks

Abstract

Motivation The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats. Over the past two decades, numerous tools and databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these tools are web-based and not well-suited for large-scale genomic data analysis.

Results To address this issue, we introduce 3Dmapper, a stand-alone command-line tool developed in Python and R. It systematically maps annotated protein positions and variants to protein structures, providing a solution that is both efficient and reliable.

Availability and implementation https://github.com/vicruiser/3Dmapper