Abstract
BackgroundThe Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function analysis. In CRISPR/Cas, RNA guides Cas nuclease to the target site to perform DNA modification.ResultsThe performance of CRISPR/Cas depends on well-designed single guide RNA (sgRNA). However, the off-target effect of sgRNA leads to undesired mutations in genome and limits the use of CRISPR/Cas. Here, we present OffScan, a universal and fast CRISPR off-target detection tool.ConclusionsOffScan is not limited by the number of mismatches and allows custom protospacer-adjacent motif (PAM), which is the target site by Cas protein. Besides, OffScan adopts the FM-index, which efficiently improves query speed and reduce memory consumption.
Highlights
The Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function analysis
Since GuideScan [18] does not include a protospacer-adjacent motif (PAM) scan model, we used the results of a popular single guide RNA (sgRNA) design tool, CRISPR-DO [15], for comparison
OffScan can find a comparable number of candidate target sites compared with CRISPR-DO
Summary
The Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function analysis. Some studies have shown that CRISPR/Cas9 non- cleave DNA sites with several mismatches, generating off-target mutations with considerable frequency [4–9]. Finding target sites can generally be accomplished quite by scanning the whole genome for the PAM sequence, such as 5′-NGG-3′ for the CRISPR/ Cas9 system. As mentioned in CRISPR-DO [15], for each candidate sgRNA k-mer in K, alignment tools have to scan the entire genome once to identify its off-target sites, rather than searching in K, which results in a large amount of redundant computations.
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