OrthoGather: a local platform for orthology-based proteome and proteomics comparisons and Gene Ontology enrichment

MotivationComparative proteomic analysis may reveal common and unique pathways regulated by the same stimulus across species using data from differential protein expression studies or curated protein sets. Functional annotations are key but vary in quality, as many proteins, particularly in prokaryotes and non-model eukaryotes, are poorly or inconsistently annotated, complicating comparative studies. Orthology inference provides a robust framework to address this, but existing tools require technical expertise, command-line use, and manual processing of complex outputs, creating barriers for researchers without computational training. ResultsWe developed OrthoGather, a locally hosted web application that streamlines comparative proteomic analysis by integrating homologous protein groups across species and Gene Ontology (GO) enrichment. It leverages functional annotations from any orthogroup member to enable functional inference even when individual species lack comprehensive annotation. Its flexible design supports cross-species exploration of conserved and unique orthogroups across proteomes or user-defined protein sets, revealing functional patterns through orthogroup relationships. OrthoGather generates publication-ready, easy-to-interpret outputs including downloadable graphs and data files, lowering barriers for researchers without computational expertise. Availability and implementationSource code, documentation and tutorials are available at Zenodo (https://doi.org/10.5281/zenodo.18603238) and GitHub (https://github.com/CarlosVivasR/OrthoGather). Supplementary materials, including the example dataset analysis are available online at Bioinformatics.