ArticleBioinformatics (Oxford, England)2016
GeneValidator: identify problems with protein-coding gene predictions.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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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
26 citing papers in PubMed.
- Genomic identification of conservation areas amid lineage divergence and admixture in a threatened island gecko.BMC biology · 2025Article
- Leveraging Synteny to Generate Reference Genomes for Conservation: Assembling the Genomes of Hector's and Māui Dolphins.Molecular ecology resources · 2025Article
- Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq.Genome research · 2025Article
- zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.Nucleic acids research · 2025Article
- zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters.bioRxiv : the preprint server for biology · 2024Article
- The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio.BMC genomic data · 2024Article
- Proteogenomic Gene Structure Validation in the Pineapple Genome.Journal of proteome research · 2024Article
- A standard workflow for community-driven manual curation ofPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- Galba: genome annotation with miniprot and AUGUSTUS.BMC bioinformatics · 2023Article
- Genomic virulence features of Beauveria bassiana as a biocontrol agent for the mountain pine beetle population.BMC genomics · 2023Article
- A state-of-the-art methodology for high-throughput in silico vaccine discovery against protozoan parasites and exemplified with discovered candidates for Toxoplasma gondii.Scientific reports · 2023Article
- GALBA: Genome Annotation with Miniprot and AUGUSTUS.bioRxiv : the preprint server for biology · 2023Article
- CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach.Journal of fungi (Basel, Switzerland) · 2023Article
- A chromosome-level assembly of the widely used Rockefeller strain of Aedes aegypti, the yellow fever mosquito.G3 (Bethesda, Md.) · 2022Article
- Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule.Communications biology · 2022Article
- Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium.Nature communications · 2022Article
- Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes.BMC bioinformatics · 2020Article
- The mole genome reveals regulatory rearrangements associated with adaptive intersexuality.Science (New York, N.Y.) · 2020Article
- High-Quality Assemblies for Three Invasive Social Wasps from theG3 (Bethesda, Md.) · 2020Article
- A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms.BMC genomics · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
unlabelled: Genomes of emerging model organisms are now being sequenced at very low cost. However, obtaining accurate gene predictions remains challenging: even the best gene prediction algorithms make substantial errors and can jeopardize subsequent analyses. Therefore, many predicted genes must be time-consumingly visually inspected and manually curated. We developed GeneValidator (GV) to automatically identify problematic gene predictions and to aid manual curation. For each gene, GV performs multiple analyses based on comparisons to gene sequences from large databases. The resulting report identifies problematic gene predictions and includes extensive statistics and graphs for each prediction to guide manual curation efforts. GV thus accelerates and enhances the work of biocurators and researchers who need accurate gene predictions from newly sequenced genomes. AVAILABILITY AND IMPLEMENTATION: GV can be used through a web interface or in the command-line. GV is open-source (AGPL), available at https://wurmlab.github.io/tools/genevalidator CONTACT: : y.wurm@qmul.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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