دورية أكاديمية
أعرض في EDS

GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.

التفاصيل البيبلوغرافية
العنوان: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.
المؤلفون: Brůna T; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Lomsadze A; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Borodovsky M; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; borodovsky@gatech.edu.; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
المصدر: Genome research [Genome Res] 2024 Jun 25; Vol. 34 (5), pp. 757-768. Date of Electronic Publication: 2024 Jun 25.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural
اللغة: English
بيانات الدورية: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9518021 Publication Model: Electronic Cited Medium: Internet ISSN: 1549-5469 (Electronic) Linking ISSN: 10889051 NLM ISO Abbreviation: Genome Res Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press, c1995-
مواضيع طبية MeSH: Molecular Sequence Annotation*/methods, Animals ; Software ; Genome ; Genomics/methods ; Eukaryota/genetics ; Algorithms
مستخلص: 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.
(© 2024 Brůna et al.; Published by Cold Spring Harbor Laboratory Press.)
التعليقات: Update of: bioRxiv. 2024 Apr 17:2023.01.13.524024. doi: 10.1101/2023.01.13.524024. (PMID: 36711453)
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معلومات مُعتمدة: R01 GM128145 United States GM NIGMS NIH HHS
تواريخ الأحداث: Date Created: 20240612 Date Completed: 20240625 Latest Revision: 20240709
رمز التحديث: 20240709
مُعرف محوري في PubMed: PMC11216313
DOI: 10.1101/gr.278373.123
PMID: 38866548
قاعدة البيانات: MEDLINE
الوصف
تدمد:1549-5469
DOI:10.1101/gr.278373.123