Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites

Jeongbin Park; Sangsu Bae; Jin-Soo Kim

doi:10.1093/bioinformatics/btv537

Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites

Bioinformatics. 2015 Dec 15;31(24):4014-6. doi: 10.1093/bioinformatics/btv537. Epub 2015 Sep 10.

Authors

Jeongbin Park¹, Sangsu Bae², Jin-Soo Kim³

Affiliations

¹ Department of Chemistry.
² Department of Chemistry, Institute for Materials Design, Hanyang University, Seoul, South Korea.
³ Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea and Department of Chemistry, Seoul National University, Seoul, South Korea.

PMID: 26358729
DOI: 10.1093/bioinformatics/btv537

Abstract

We present Cas-Designer, a user-friendly program to aid researchers in choosing appropriate target sites in a gene of interest for type II CRISPR/Cas-derived RNA-guided endonucleases, which are now widely used for biomedical research and biotechnology. Cas-Designer rapidly provides the list of all possible guide RNA sequences in a given input DNA sequence and their potential off-target sites including bulge-type sites in a genome of choice. In addition, the program assigns an out-of-frame score to each target site to help users choose appropriate sites for gene knockout. Cas-Designer shows the results in an interactive table and provides user-friendly filter functions.

Availability and implementation: Free access at http://rgenome.net/cas-designer/.

Publication types

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

MeSH terms

CRISPR-Associated Proteins*
CRISPR-Cas Systems*
Clustered Regularly Interspaced Short Palindromic Repeats
Endodeoxyribonucleases*
Gene Knockout Techniques*
Genome
Internet
RNA / chemistry
Sequence Analysis, DNA / methods*
Software*

Substances

CRISPR-Associated Proteins
RNA
Endodeoxyribonucleases