Abstract
CRISPR/Cas9 technology is revolutionizing the field of gene editing. While this technology enables the targeting of any gene, it may also target unplanned loci, termed off-target sites (OTS), which are a few mismatches, insertions, and deletions from the target. While existing methods for finding OTS up to a given mismatch threshold are efficient, other methods considering insertions and deletions are limited by long runtimes, incomplete OTS lists, and partial support of versatile thresholds. Here, we developed SWOffinder, an efficient method based on Smith-Waterman alignment to find all OTS up to some edit distance. We implemented an original trace-back approach to find OTS under versatile criteria, such as separate limits on the number of insertions, deletions, and mismatches. Compared to state-of-the-art methods, only SWOffinder finds all OTS in the genome in just a few minutes. SWOffinder enables accurate and efficient genomic search of OTS, which will lead to safer gene editing.
Original language | English |
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Article number | 108557 |
Journal | iScience |
Volume | 27 |
Issue number | 1 |
DOIs | |
State | Published - 19 Jan 2024 |
Bibliographical note
Publisher Copyright:© 2023 The Author(s)
Funding
This study was partially supported by the Israel Science Foundation (grant no. 358/21 ). We gratefully acknowledge the support of the CRISPR-IL consortium for supporting our research and for giving access to the AWS platform used for part of this work. Ofir acknowledges the support of the Azrieli PhD fellowship , the Kretiman PhD fellowship at Ben-Gurion University , Nehemia Levtzion Ph.D. fellowship from the Israeli Council for Higher Education , and the cloud-compute credit by the Planning and Budgeting Committee through IUCC.
Funders | Funder number |
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Israel Science Foundation | 358/21 |
Council for Higher Education |
Keywords
- Algorithms
- Bioinformatics
- Biological constraints
- Techniques in genetics