Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies

Genome Biology - Tập 25 - Trang 1-4 - 2024
Shujun Ou1, Ning Jiang2, Candice N. Hirsch3, Matthew B. Hufford4
1Department of Molecular Genetics, Ohio State University, Columbus, USA
2Department of Horticulture, Michigan State University, East Lansing, USA.
3Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, USA
4Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA

Tài liệu tham khảo

Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 2019;20:275. Gozashti L, Hoekstra HE. Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome Biol. 2023. Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11. Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA. 2020;117(17):9451–7. Li Y, Jiang N, Sun Y. AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes. Plant Physiol. 2022;188(2):955–70.
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Genome Biology

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