Easy-Prime: a machine learning–based prime editor design tool

Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime, a machine learning–based program trained with multiple published data sources. Easy-Prime...

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Detalles Bibliográficos
Autores principales: Li, Yichao, Chen, Jingjing, Tsai, Shengdar Q., Cheng, Yong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8377858/
https://www.ncbi.nlm.nih.gov/pubmed/34412673
http://dx.doi.org/10.1186/s13059-021-02458-0
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author Li, Yichao
Chen, Jingjing
Tsai, Shengdar Q.
Cheng, Yong
author_facet Li, Yichao
Chen, Jingjing
Tsai, Shengdar Q.
Cheng, Yong
author_sort Li, Yichao
collection PubMed
description Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime, a machine learning–based program trained with multiple published data sources. Easy-Prime captures both known and novel features, such as RNA folding structure, and optimizes feature combinations to improve editing efficiency. We provide optimized PE design for installation of 89.5% of 152,351 GWAS variants. Easy-Prime is available both as a command line tool and an interactive PE design server at: http://easy-prime.cc/. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02458-0.
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spelling pubmed-83778582021-08-23 Easy-Prime: a machine learning–based prime editor design tool Li, Yichao Chen, Jingjing Tsai, Shengdar Q. Cheng, Yong Genome Biol Software Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime, a machine learning–based program trained with multiple published data sources. Easy-Prime captures both known and novel features, such as RNA folding structure, and optimizes feature combinations to improve editing efficiency. We provide optimized PE design for installation of 89.5% of 152,351 GWAS variants. Easy-Prime is available both as a command line tool and an interactive PE design server at: http://easy-prime.cc/. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02458-0. BioMed Central 2021-08-19 /pmc/articles/PMC8377858/ /pubmed/34412673 http://dx.doi.org/10.1186/s13059-021-02458-0 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Li, Yichao
Chen, Jingjing
Tsai, Shengdar Q.
Cheng, Yong
Easy-Prime: a machine learning–based prime editor design tool
title Easy-Prime: a machine learning–based prime editor design tool
title_full Easy-Prime: a machine learning–based prime editor design tool
title_fullStr Easy-Prime: a machine learning–based prime editor design tool
title_full_unstemmed Easy-Prime: a machine learning–based prime editor design tool
title_short Easy-Prime: a machine learning–based prime editor design tool
title_sort easy-prime: a machine learning–based prime editor design tool
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8377858/
https://www.ncbi.nlm.nih.gov/pubmed/34412673
http://dx.doi.org/10.1186/s13059-021-02458-0
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