ArticleLife (Basel, Switzerland)2015
A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes.
Article in Life (Basel, Switzerland), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- ProtPen combines sequence- and structure-based approaches to facilitate protein function predictions on a proteome-wide scale.bioRxiv : the preprint server for biology · 2026Article
- Expanding kinetoplastid genome annotation through protein structure comparison.PLoS pathogens · 2025Article
- From genes to Black Rust: genomic insights into corrosive methanogens.FEMS microbes · 2025Article
- Identification of structural and regulatory cell-shape determinants in Haloferax volcanii.Nature communications · 2024Article
- Iron starvation results in up-regulation of a probableFrontiers in microbiology · 2024Article
- Article
- Genomic and Bioinformatic Resources for Perennial Fruit Species.Current genomics · 2022Review
- Ecosystem-specific microbiota and microbiome databases in the era of big data.Environmental microbiome · 2022Review
- Genomic analysis of heavy metal-resistant Halobacterium salinarum isolated from Sfax solar saltern sediments.Extremophiles : life under extreme conditions · 2022Article
- A crowdsourcing open platform for literature curation in UniProt.PLoS biology · 2021Article
- Open Issues for Protein Function Assignment inGenes · 2021Article
- Mantis: flexible and consensus-driven genome annotation.GigaScience · 2021Article
- CODON-Software to manual curation of prokaryotic genomes.PLoS computational biology · 2021Article
- Cellular and Genomic Properties ofFrontiers in microbiology · 2021Article
- Regulated Iron Siderophore Production of the Halophilic ArchaeonBiomolecules · 2020Article
- Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases.Genomics, proteomics & bioinformatics · 2020Article
- Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754MicrobiologyOpen · 2020Article
- The Genome Sequence of the Halobacterium salinarum Type Strain Is Closely Related to That of Laboratory Strains NRC-1 and R1.Microbiology resource announcements · 2019Article
- ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.PLoS neglected tropical diseases · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis, Haloquadratum walsbyi strains HBSQ001 and C23, Natrialba magadii, Haloarcula marismortui and Har. hispanica, and Halohasta litchfieldiae). Genomes are checked for missing genes, start codon misassignments, and disrupted genes. Assignments of a specific function are preferably based on experimentally characterized homologs (Gold Standard Proteins). To avoid overannotation, which is a major source of database errors, we restrict annotation to only general function assignments when support for a specific substrate assignment is insufficient. This strategy results in annotations that are resistant to the plethora of errors that compromise public databases. Annotation consistency is rigorously validated for ortholog pairs from the genomes surveyed. The annotation is regularly crosschecked against the UniProt database to further improve annotations and increase the level of standardization. Enhanced genome annotations are submitted to public databases (EMBL/GenBank, UniProt), to the benefit of the scientific community. The enhanced annotations are also publically available via HaloLex.
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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.