quercusTOA-APP: A Desktop Application for Oak Functional Annotation and Comparative Genomics

Description quercusTOA-APP is a versatile desktop application designed to streamline functional annotation, enrichment analysis, and comparative genomics for Quercus species. By leveraging the cross-referenced data hosted in the quercusTOA database (Mora-Márquez et al., 2026), the app provides a user-friendly interface to process transcriptomic and proteomic data from oak experiments with minimal manual intervention. Built in Python 3, the application features a graphical user interface (GUI) compatible with Linux, Windows, and macOS. It also includes BASH scripts for high-performance execution on Linux servers. Key Features Automated Setup: Manages the installation of third-party dependencies and synchronizes the latest database versions directly from remote repositories. Comparative Genomics: * Homology searches by protein ID or sequence across multiple oak lineages. Automated generation of FASTA files, multiple sequence alignments (MAFFT), and phylogenetic trees. Mapping of annotations onto user-supplied genome assemblies using any database species as a reference via LIFTOFF. Functional Annotation & Enrichment: High-speed homology searches (BLAST/DIAMOND) against optimized oak protein sets. Retrieval of comprehensive functional features (GO terms, KEGG, MetaCyc, EC numbers, etc.). Identification of Arabidopsis thaliana (TAIR10) orthologs. Technical Specifications Core Engine: Python 3. Inherited Utilities: Built upon the robust framework of gymnoTOA-APP, optimized for the specific genomic architecture of the Quercus genus. Repository & Updates: The source code and latest updates are maintained at https://github.com/GGFHF/quercusTOA-app. How to Cite If you use this software, please cite both the application and the underlying database: Software: Mora-Márquez, F., Hurtado, M. & López de Heredia, U. quercusTOA-APP (Quercus Taxonomy-oriented Annotation). Zenodo [DOI: 10.5281/zenodo.18740268] (2026). Database: Mora-Márquez, F., Hurtado, M. & López de Heredia, U. quercusTOA database: Integrating functional annotations and comparative genomics across oak lineages. Zenodo [DOI: 10.5281/zenodo.18712996] (2026).