ArticleBMC genomics2020
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Validation of the International Weed Genomics Consortium genome annotation pipeline through reannotation of the model species Arabidopsis thaliana.The plant genome · 2026Article
- Genome Assemblies for Seven Families of Birds From the Global South.Molecular ecology resources · 2026Article
- Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species.Proteomics · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics.Molecular biology and evolution · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
- OMAnnotator: a novel approach to building an annotated consensus genome sequence.Bioinformatics advances · 2026Article
- mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset.Nature communications · 2025Article
- HydraRNA: a hybrid architecture based full-length RNA language model.Genome biology · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model.BMC bioinformatics · 2025Article
- Annotation matters: the effect of structural gene annotation on orthology inference.Bioinformatics (Oxford, England) · 2025Article
- Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq.Genome research · 2025Article
- Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.Nature communications · 2025Article
- Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus.Journal of animal science and biotechnology · 2025Article
- zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.Nucleic acids research · 2025Article
- An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions.Bioinformatics advances · 2025Review
- A genomic database furnishes minimal functional glycyl-tRNA synthetases homologous to other, designed class II urzymes.Nucleic acids research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
backgroundThe draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed to evaluate the accuracy of gene prediction methods in the face of incomplete genome assemblies, low genome coverage and quality, complex gene structures, or a lack of suitable sequences for evidence-based annotations.
resultsWe describe the construction of a new benchmark, called G3PO (benchmark for Gene and Protein Prediction PrOgrams), designed to represent many of the typical challenges faced by current genome annotation projects. The benchmark is based on a carefully validated and curated set of real eukaryotic genes from 147 phylogenetically disperse organisms, and a number of test sets are defined to evaluate the effects of different features, including genome sequence quality, gene structure complexity, protein length, etc. We used the benchmark to perform an independent comparative analysis of the most widely used ab initio gene prediction programs and identified the main strengths and weaknesses of the programs. More importantly, we highlight a number of features that could be exploited in order to improve the accuracy of current prediction tools.
conclusionsThe experiments showed that ab initio gene structure prediction is a very challenging task, which should be further investigated. We believe that the baseline results associated with the complex gene test sets in G3PO provide useful guidelines for future studies.
Indexed as
Identifiers
What OpenQuestion holds
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.