Genome-wide tool for sensitive de novo identification of interspersed and tandem repeats
Authors/Creators
- 1. Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
Contributors
Researcher:
- 1. Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
Description
Genomic repeats are functionally ubiquitous structural units found in all genomes. These repeating patterns have a manifold signature and structure, making identification challenging. To address this challenge, we developed software that can rapidly and accurately detect any type of repeated sequences de novo in genomic sequences in the form of interspersed or clustered repeats. Numerous forms of repeated sequences and “repeat within repeat” patterns can be identified even for very complex sequence variants and for implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any type of short- or long-tandem repeats belonging to a wide range of organized into higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool significantly contributes to elucidating the intricate landscape of genomic repeats.
Notes
Files
Result.zip
Files
(296.4 MB)
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Additional details
References
- Belyayev, A., et al. The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms. Mob DNA 2022;13(1):8.
- Campagna, D., et al. RAP: a new computer program for de novo identification of repeated sequences in whole genomes. Bioinformatics 2005;21(5):582-588.
- Dalikova, M., et al. The Role of Repetitive Sequences in Repatterning of Major Ribosomal DNA Clusters in Lepidoptera. Genome Biol Evol 2023;15(6).
- Girgis, H.Z. Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics 2015;16:227.
- Gluncic, M., et al. Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution. Life Sci Alliance 2023;6(1).
- Kalendar, R., et al. Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants. Int J Mol Sci 2020;21(8).
- Kazazian, H.H., Jr. Mobile elements: drivers of genome evolution. Science 2004;303(5664):1626-1632.
- Kojima, K.K. Human transposable elements in Repbase: genomic footprints from fish to humans. Mob DNA 2018;9:2.
- Lerat, E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity (Edinb) 2010;104(6):520-533.
- Lexa, M., et al. HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization. Bioinformatics 2022;38(16):4030-4032.
- Liao, X., et al. RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads. BMC Bioinformatics 2020;21(1):463.
- Liao, X., et al. A sensitive repeat identification framework based on short and long reads. Nucleic Acids Res 2021;49(17):e100.
- Novak, P., et al. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 2013;29(6):792-793.
- Pulido, M. and Casacuberta, J.M. Transposable element evolution in plant genome ecosystems. Curr Opin Plant Biol 2023;75:102418.
- Rodriguez, F. and Arkhipova, I.R. An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes. Methods Mol Biol 2023;2607:1-23.
- Seah, B.K.B., et al. MITE infestation accommodated by genome editing in the germline genome of the ciliate Blepharisma. Proc Natl Acad Sci U S A 2023;120(4):e2213985120.