ArticleNucleic acids research2024
RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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.
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
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.Cell host & microbe · 2025Pooled it
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- Anaerobic riboflavin degradation by human gutJournal of bacteriology · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.Nature biotechnology · 2026Article
- Novel transposon TnMicrobial genomics · 2026Article
- Structural and immunogenic evaluation of silk proteins from Bombyx mori using advanced bioinformatics and deep learning for biomaterials applications.Journal, genetic engineering & biotechnology · 2026Article
- Whole genome sequence datasets ofData in brief · 2026Article
- Complete genome of marine flavobacteriumMicrobiology resource announcements · 2026Article
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs.Nucleic acids research · 2026Article
- Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids.Nature microbiology · 2026Article
- Novel transposon TnmedRxiv : the preprint server for health sciences · 2026Article
- Anaerobic riboflavin degradation by human gutbioRxiv : the preprint server for biology · 2026Article
- Complete genome sequence of a newMicrobiology resource announcements · 2026Article
- Within-Host Environmental Heterogeneity Is Associated With Phenotypic but Not Genomic Diversity in Wolbachia Endosymbionts.Environmental microbiology reports · 2026Article
- Niche specialization and cross-feeding interactions shaping gut microbial fiber degradation in a model omnivore.bioRxiv : the preprint server for biology · 2026Article
- Metabolic potential structures gill symbiont communities in two common shipworm species.The ISME journal · 2026Article
- Article
- RefSeq-corrected transcriptomic and RNA-interaction integration maps medium-associated vancomycin response rewiring inFrontiers in microbiology · 2026Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains over 315 000 bacterial and archaeal genomes and 236 million proteins with up-to-date and consistent annotation. In the past 3 years, we have expanded the diversity of the RefSeq collection by including the best quality metagenome-assembled genomes (MAGs) submitted to INSDC (DDBJ, ENA and GenBank), while maintaining its quality by adding validation checks. Assemblies are now more stringently evaluated for contamination and for completeness of annotation prior to acceptance into RefSeq. MAGs now account for over 17000 assemblies in RefSeq, split over 165 orders and 362 families. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP), which is used to annotate nearly all RefSeq assemblies include better detection of protein-coding genes. Nearly 83% of RefSeq proteins are now named by a curated Protein Family Model, a 4.7% increase in the past three years ago. In addition to literature citations, Enzyme Commission numbers, and gene symbols, Gene Ontology terms are now assigned to 48% of RefSeq proteins, allowing for easier multi-genome comparison. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/. PGAP is available as a stand-alone tool able to produce GenBank-ready files at https://github.com/ncbi/pgap.
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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.