CHOPCHOP v2: A Web Tool for the Next Generation of CRISPR Genome Engineering

Nucleic Acids Res. 2016 Jul 8;44(W1):W272-6. doi: 10.1093/nar/gkw398. Epub 2016 May 16.

Abstract

In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no.

MeSH terms

  • Animals
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • CRISPR-Associated Protein 9
  • CRISPR-Cas Systems*
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Deoxyribonuclease I / genetics
  • Deoxyribonuclease I / metabolism
  • Endonucleases / genetics*
  • Endonucleases / metabolism
  • Gene Editing
  • Genome*
  • Humans
  • Information Storage and Retrieval
  • Internet
  • Nucleotide Motifs
  • RNA, Guide / chemical synthesis*
  • RNA, Guide / genetics
  • Software*
  • Transcription Activator-Like Effector Nucleases / genetics
  • Transcription Activator-Like Effector Nucleases / metabolism

Substances

  • Bacterial Proteins
  • RNA, Guide
  • CRISPR-Associated Protein 9
  • Cas9 endonuclease Streptococcus pyogenes
  • Endonucleases
  • Transcription Activator-Like Effector Nucleases
  • Deoxyribonuclease I