ArticleGenome research2024
GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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125 citing papers in PubMed.
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- Efficient evidence-based genome annotation with EviAnn.Nature methods · 2026Article
- Telomere-to-telomere genome assembly of pumpkin (Horticulture research · 2026Article
- Evolution of compound eye cell types shapes visual behaviors acrossbioRxiv : the preprint server for biology · 2026Article
- Pipettes and Pipelines: The Weapons of Omics Sciences for a New Age of Clinical Studies.Current issues in molecular biology · 2026Review
- Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis ofHorticulture research · 2026Article
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- Comprehensive genomic analysis reveals the class II diterpene cyclases in Dodonaea viscosa.Phytochemistry · 2026Article
- A Complete Telomere-To-Telomere Assembly ofEvolutionary applications · 2026Article
- Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model.Communications biology · 2026Article
65 more citing papers are in PubMed but not listed here.
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Abstract
Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic-, and protein-derived evidence that has been developed with a focus on large plant and animal genomes. GeneMark-ETP first identifies genomic loci where extrinsic data are sufficient for making gene predictions with "high confidence." The genes situated in the genomic space between the high-confidence genes are predicted in the next stage. The set of high-confidence genes serves as an initial training set for the statistical model. Further on, the model parameters are iteratively updated in the rounds of gene prediction and parameter re-estimation. Upon reaching convergence, GeneMark-ETP makes the final predictions and delivers the whole complement of predicted genes. GeneMark-ETP outperforms gene finders using a single type of extrinsic evidence. Comparisons with gene finders MAKER2 and TSEBRA, those that use both transcript- and protein-derived extrinsic evidence, show that GeneMark-ETP delivers state-of-the-art gene-prediction accuracy, with the margin of outperforming existing approaches increasing in its application to larger and more complex eukaryotic genomes.
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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 Socratic graph.