ArticleDatabase : the journal of biological databases and curation2025
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms.
Article in Database : the journal of biological databases and curation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 2 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
2 citing papers in PubMed.
- quercusTOA: integrating functional annotations and comparative genomics across oak lineages.Frontiers in bioinformatics · 2026Article
- An enhanced gene function analysis platform for Gastrodia Elata integrating further omics data and analysis tools.BMC plant biology · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gymnosperms are a clade of non-flowering plants that include about 1000 living species. Due to their complex genomes and lack of genomic resources, functional annotation in genomics and transcriptomics on gymnosperms suffers from limitations. Here we present gymnotoa-db, which is a novel, publicly accessible relational database designed to facilitate functional annotation in gymnosperms. This database stores non-redundant records of gymnosperm proteins, encompassing taxonomic and functional information. The complementary software, gymnotoa-app, enables users to download gymnotoa-db and execute a comprehensive functional annotation pipeline for high-throughput sequencing-derived DNA or cDNA sequences. gymnotoa-app's user-friendly interface and efficient algorithms streamline the functional annotation process, making it an invaluable tool for researchers studying gymnosperms. We compared gymnotoa-app's performance against other annotation tools utilizing disparate reference databases. Our results demonstrate gymnotoa-app's superior ability to accurately annotate gymnosperm transcripts, recovering a greater number of transcripts and unique, non-redundant Gene Ontology terms. gymnotoa-db's distinctive features include comprehensive coverage with a non-redundant dataset of gymnosperm protein sequences, robust functional information that integrates data from multiple ontology systems, including GO, KEGG, EC, and MetaCYC, while keeping the taxonomic context, including Arabidopsis homologs. Database URL: https://blogs.upm.es/gymnotoa-db/2024/09/19/gymnotoa-app/.
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