fastCDS: proteome-scale mapping of protein domains to genomic coordinates

Abstract

SummaryMapping protein regions to genomic coordinates underpins the study of exon architecture and the interpretation of clinical variants in their exon context. Existing tools resolve individual queries accurately but scale poorly to proteome-wide analyses. We present fastCDS, a C++ toolkit with command line and Python interfaces for rapid protein-to-genome coordinate mapping from GTF annotations. It matches the accuracy of existing methods while running at least two to three orders of magnitude faster. Mapping all human Pfam domains in seconds, we used the resulting atlas to examine how exonic architecture varies with domain function. Availability and ImplementationfastCDS is freely available under the MIT license at {{https://github.com/SotoLF/fastCDS}} and can be installed with pip install fastCDS or mamba install -c bioconda fastCDS. Pre-built GTF genome indices are archived at Zenodo, DOI: https://zenodo.org/records/21436146. Contactlsoto@rockefeller.edu Supplementary InformationSupplementary data are available at Bioinformatics online.