title: CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering.
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.
authors.affiliation: Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway.
authors.forename: Kornel
authors.initials: K
authors.lastname: Labun
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Tessa G
authors.initials: TG
authors.lastname: Montague
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Gagnon
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Summer B
authors.initials: SB
authors.lastname: Thyme
authors.affiliation: Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway eivind.valen@gmail.com.
authors.forename: Eivind
authors.initials: E
authors.lastname: Valen
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D000076987:CRISPR-Associated Protein 9; D064113:CRISPR-Cas Systems; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D003850:Deoxyribonuclease I / Q000235:genetics / Q000378:metabolism; D004720:Endonucleases / Q000235:genetics* / Q000378:metabolism; D000072669:Gene Editing; D016678:Genome; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D059372:Nucleotide Motifs; D000094704:RNA, Guide, CRISPR-Cas Systems / Q000138:chemical synthesis* / Q000235:genetics; D012984:Software; D000069896:Transcription Activator-Like Effector Nucleases / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D000094704:RNA, Guide, CRISPR-Cas Systems; D000076987:CRISPR-Associated Protein 9; C000606107:Cas9 endonuclease Streptococcus pyogenes; D004720:Endonucleases; D000069896:Transcription Activator-Like Effector Nucleases; D003850:Deoxyribonuclease I