ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2023
GINGER: an integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos.The New phytologist · 2026Article
- MarpolBase: genome database for Marchantia polymorpha featuring high quality reference genome sequences.Plant & cell physiology · 2026Article
- Whole genome analysis of toxic Papilionidae butterflies utilizing aristolochic acid, Pachliopta aristolochiae, and Byasa alcinous.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes.iScience · 2025Article
- The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid WheatbioRxiv : the preprint server for biology · 2025Article
- Evolution and functioning of an X-A balance sex-determining system in hops.Nature plants · 2025Article
- Whole-genome sequencing of the ant Crematogaster osakensis (Hymenoptera: Formicidae: Myrmicinae).DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- The impact of telomere-to-telomere genome assembly in the plant pan-genomics era.Breeding science · 2025Article
- Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes.Scientific data · 2023Article
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Authors and funding
10 authors.
Funding
Abstract
The prediction of gene structure within the genome sequence is the starting point of genome analysis, and its accuracy has a significant impact on the quality of subsequent analyses. Gene structure prediction is roughly divided into RNA-Seq-based methods, ab initio-based methods, homology-based methods, and the integration of individual prediction methods. Integrated methods are mainstream in recent genome projects because they improve prediction accuracy by combining or taking the best individual prediction findings; however, adequate prediction accuracy for eukaryotic species has not yet been achieved. Therefore, we developed an integrated tool, GINGER, that solves various issues related to gene structure prediction in higher eukaryotes. By handling artefacts in alignments of RNA and protein sequences, reconstructing gene structures via dynamic programming with appropriately weighted and scored exon/intron/intergenic regions, and applying different prediction processes and filtering criteria to multi-exon and single-exon genes, we achieved a significant improvement in accuracy compared to the existing integration methods. The feature of GINGER is its high prediction accuracy at the gene and exon levels, which is pronounced for species with more complex gene architectures. GINGER is implemented using Nextflow, which allows for the efficient and effective use of computing resources.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.