Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1

Jeongbin Park; Sangsu Bae

doi:10.1093/bioinformatics/btx695

Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1

Bioinformatics. 2018 Mar 15;34(6):1077-1079. doi: 10.1093/bioinformatics/btx695.

Authors

Jeongbin Park¹, Sangsu Bae^{1

2}

Affiliations

¹ Department of Chemistry, Hanyang University, Seoul 04763, South Korea.
² Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, South Korea.

PMID: 29186338
DOI: 10.1093/bioinformatics/btx695

Abstract

Summary: Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time.

Availability and implementation: Free access at http://www.rgenome.net/cpf1-database/.

Contact: sangsubae@hanyang.ac.kr.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Endonucleases / metabolism
Gene Editing
Gene Knockout Techniques
Genome
Genomic Library*
Internet
RNA, Guide, CRISPR-Cas Systems / genetics

Substances

RNA, Guide, CRISPR-Cas Systems
Endonucleases