ArticleNucleic acids research2010
FragGeneScan: predicting genes in short and error-prone reads.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 440 papers.
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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.
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Who cites it
440 citing papers in PubMed.
- Trial
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- DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.Briefings in bioinformatics · 2026Article
- Metagenomic insights into mangrove lignocellulolytic bacteria and functional analysis of a glucose-tolerant GH 1 β-glucosidase.3 Biotech · 2026Article
- Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.Animal microbiome · 2026Article
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- Mixing regimes shape microbial community composition, nutrient regimes, and plant growth attributes in Jeevamrit: metagenomics and culturomics-based insights.Scientific reports · 2026Article
- Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.The ISME journal · 2026Article
- Multi-feature fusion for gene prediction and functional peptide identification.Frontiers in microbiology · 2026Article
- Species-specific rumen microbial responses to dietary inhibition of methanogenesis in cows and goats.Frontiers in microbiology · 2026Article
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- Multi-domain temporal patterns reveal stable community membership but dynamic interactions in the coastal microbiome.Environmental microbiome · 2025Article
- Dynamics of the transcriptomic landscape of OsHV-1 replication in haemocytes of the Pacific oyster (The Journal of general virology · 2025Article
- Plastic Type and Condition Have Minimal Impact on Associated Marine Biofilm Communities.Environmental microbiology · 2025Article
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- Targeted assembly recovers high ammonia monooxygenase diversity in mudflat intertides.mSystems · 2025Article
380 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging problem in annotating metagenomes, since the assembly of metagenomes is often not available. Gene predictors developed for whole genomes (e.g. Glimmer) and recently developed for metagenomic sequences (e.g. MetaGene) show a significant decrease in performance as the sequencing error rates increase, or as reads get shorter. We have developed a novel gene prediction method FragGeneScan, which combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads. The performance of FragGeneScan was comparable to Glimmer and MetaGene for complete genomes. But for short reads, FragGeneScan consistently outperformed MetaGene (accuracy improved ∼62% for reads of 400 bases with 1% sequencing errors, and ∼18% for short reads of 100 bases that are error free). When applied to metagenomes, FragGeneScan recovered substantially more genes than MetaGene predicted (>90% of the genes identified by homology search), and many novel genes with no homologs in current protein sequence database.
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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.