PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations.

ABSTRACT:

Summary

Single-guide RNAs (sgRNAs) targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state of the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports homology-directed repair template generation for genome editing experiments and the visualization of the mutated amino acids in 3D.

Availability and implementation

PAVOOC is available under https://pavooc.me and accessible using modern browsers (Chrome/Chromium rec

SUBMITTER: Schaefer M 

PROVIDER: S-EPMC6596878 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature