gymnotoa-db: a database and application to optimize functional annotation in gymnosperms

• DOI: 10.1093/database/baaf019
• Publication Date: 2025-03-07T10:52:31Z
• Authors: Fernando Mora-Már...; Mikel Hurtado; Unai López de Her...
• Keywords: Gymnosperm; KEGG; Functional Genomics; Gene Annotation

Gymnosperms are a clade of non-flowering plants that include about 1000 living species. Due to their complex genomes and lack genomic resources, functional annotation in genomics transcriptomics on gymnosperms suffers from limitations. Here we present gymnotoa-db, which is novel, publicly accessible relational database designed facilitate gymnosperms. This stores non-redundant records gymnosperm proteins, encompassing taxonomic information. The complementary software, gymnotoa-app, enables users download gymnotoa-db execute comprehensive pipeline for high-throughput sequencing-derived DNA or cDNA sequences. gymnotoa-app's user-friendly interface efficient algorithms streamline the process, making it an invaluable tool researchers studying We compared performance against other tools utilizing disparate reference databases. Our results demonstrate superior ability accurately annotate transcripts, recovering greater number transcripts unique, Gene Ontology terms. gymnotoa-db's distinctive features coverage with dataset protein sequences, robust information integrates data multiple ontology systems, including GO, KEGG, EC, MetaCYC, while keeping context, Arabidopsis homologs. Database URL: https://blogs.upm.es/gymnotoa-db/2024/09/19/gymnotoa-app/.