ArticleNucleic acids research2001
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,397 papers.
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
1,397 citing papers in PubMed, 2,336 citations in OpenAlex.
- Isolation and genomic characterization of a Teetrevirus phage infecting Klebsiella quasipneumoniae with a putative SAMase gene.Archives of virology · 2026Article
- Genomic and functional divergence analysis of closely relatedApplied and environmental microbiology · 2026Article
- Article
- Four coding-complete genomes of bovine viral diarrhea virus-2a (Microbiology resource announcements · 2026Article
- The near-complete genome sequence of vB_AgrS_573, a lyticMicrobiology resource announcements · 2026Article
- Host-Associated Differentiation in a Parasitoid Wasp Connected to Venom-Related but Not Chemosensory Genes.Molecular ecology · 2026Article
- Genomic characterization and phage cocktail suppression of a multidrug-resistantApplied and environmental microbiology · 2026Article
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- Natural occurrence of a slow lytic pseudomonas phage in a Pediatric case of multidrug-resistant P. aeruginosa severe pneumonia.Virus genes · 2026Article
- Decoding microbial metabolic complementarity from individual traits to community structuring.Ecology · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Human pegivirus 1 in healthy blood donors and in acute febrile patients from Mato Grosso, Midwestern Brazil.Archives of virology · 2026Observational
- Article
- Resolution of MALDI-TOF MS compared to whole genome sequencing for the identification of Vibrio parahaemolyticus strains isolated from oysters.Archives of microbiology · 2026Article
- Phenotypic characterization and biocontrol application of bacteriophage P53F with potent lytic and antibiofilm activities against Salmonella Pullorum.Archives of microbiology · 2026Article
- Salmonella Pullorum strain SPullorum-YN-07 from dead embryos of Yanjin black-bone chickens: Complete genome with IncFII(S) and Col(pVC) plasmids and pathogenicity.Poultry science · 2026Article
- Identification and genomic insights into a plant probiotic Bacillus subtilis strain CF1 isolated from Protaetia brevitarsis frass.BMC genomics · 2026Article
- Discovery of specific rhizosphere bacteriaScience advances · 2026Article
- Whole-genome and Comparative Genomic Analysis Reveal the Biocontrol and Plant Growth-Promoting Potential of Bacillus velezensis JN.Y2 Against Oat Anthracnose.Functional & integrative genomics · 2026Article
- Whole-genome sequencing and analysis of the endophytic fungus Alternaria alternata Y-2 from Leymus chinensis.Scientific reports · 2026Article
1,337 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
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene start prediction can be improved by combining models of protein-coding and non-coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method, called GeneMarkS, utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely 83.2% of the translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts in an experimentally validated set of Escherichia coli genes. We have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames containing real genes, with an accuracy matching the level of the best currently used gene detection methods. Accurate translation start prediction, in addition to the refinement of protein sequence N-terminal data, provides the benefit of precise positioning of the sequence region situated upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites can be revealed and analyzed with higher precision. These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed.
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.