A beginner's guide to manual curation of transposable elements

Goubert, ClementMcGill Univ, Canadian Ctr Computat Genom, Montreal, PQ, Canada.;McGill Univ, Dept Human Genet, Montreal, PQ, Canada. (författare)

Correction in: MOBILE DNA, Volume 13, Issue 1, Article Number 15, DOI 10.1186/s13100-022-00272-4
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.

Craig, Rory J.Univ Edinburgh, Inst Evolutionary Biol, Edinburgh EH9 3FL, Midlothian, Scotland. (författare)
Bilat, Agustin F.Univ Republica, Fac Med, Dept Genet, Montevideo, Uruguay. (författare)
Peona, ValentinaUppsala universitet,Systematisk biologi(Swepub:uu)valpe113 (författare)
Vogan, Aaron A.Uppsala universitet,Systematisk biologi(Swepub:uu)aarvo811 (författare)
Protasio, Anna, VDept Pathol, Tennis Court Rd, Cambridge CB1 2PQ, England.;Univ Cambridge Christs Coll, St Andrews St, Cambridge CB2 3BU, England. (författare)
McGill Univ, Canadian Ctr Computat Genom, Montreal, PQ, Canada.;McGill Univ, Dept Human Genet, Montreal, PQ, Canada.Univ Edinburgh, Inst Evolutionary Biol, Edinburgh EH9 3FL, Midlothian, Scotland. (creator_code:org_t)

Av författaren/redakt...: Goubert, Clement; Craig, Rory J.; Bilat, Agustin F ...; Peona, Valentina; Vogan, Aaron A.; Protasio, Anna, ...

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