A beginner's guide to manual curation of transposable elements.
Authors
Goubert, Clement
Craig, Rory J
Bilat, Agustin F
Peona, Valentina
Vogan, Aaron A
Protasio, Anna V
Publication Date
2022-03-30Journal Title
Mob DNA
ISSN
1759-8753
Publisher
Springer Science and Business Media LLC
Volume
13
Issue
1
Language
en
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
Goubert, C., Craig, R. J., Bilat, A. F., Peona, V., Vogan, A. A., & Protasio, A. V. (2022). A beginner's guide to manual curation of transposable elements.. Mob DNA, 13 (1) https://doi.org/10.1186/s13100-021-00259-7
Abstract
BACKGROUND: In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate these fascinating genomic elements. Many algorithms and pipelines are available to automatically identify putative TE families present in a genome. Despite the availability of these valuable resources, producing a library of high-quality full-length TE consensus sequences largely remains a process of manual curation. This know-how is often passed on from mentor-to-mentee within research groups, making it difficult for those outside the field to access this highly specialised skill. RESULTS: Our manuscript attempts to fill this gap by providing a set of detailed computer protocols, software recommendations and video tutorials for those aiming to manually curate TEs. Detailed step-by-step protocols, aimed at the complete beginner, are presented in the Supplementary Methods. CONCLUSIONS: The proposed set of programs and tools presented here will make the process of manual curation achievable and amenable to all researchers and in special to those new to the field of TEs.
Keywords
Methodology, Mobile DNA Tools
Identifiers
s13100-021-00259-7, 259
External DOI: https://doi.org/10.1186/s13100-021-00259-7
This record's URL: https://www.repository.cam.ac.uk/handle/1810/336855
Rights
Licence:
http://creativecommons.org/licenses/by/4.0/
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