title: Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes.
abstract: The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5' or 3' and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas, and the code is available upon request.
authors.affiliation: National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain.
authors.forename: Juan C
authors.initials: JC
authors.lastname: Oliveros
authors.affiliation: National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain.
authors.forename: Mònica
authors.initials: M
authors.lastname: Franch
authors.affiliation: National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Tabas-Madrid
authors.affiliation: National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain.
authors.forename: David
authors.initials: D
authors.lastname: San-León
authors.affiliation: National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain CIBERER, ISCIII, Madrid, Spain.
authors.forename: Lluis
authors.initials: L
authors.lastname: Montoliu
authors.affiliation: National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain.
authors.forename: Pilar
authors.initials: P
authors.lastname: Cubas
authors.affiliation: National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain pazos@cnb.csic.es.
authors.forename: Florencio
authors.initials: F
authors.lastname: Pazos
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D000076987:CRISPR-Associated Protein 9; D064113:CRISPR-Cas Systems; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004720:Endonucleases / Q000235:genetics* / Q000378:metabolism; D056890:Eukaryota / Q000235:genetics; D000072669:Gene Editing; D016678:Genome; D016247:Information Storage and Retrieval; D020407:Internet; D059372:Nucleotide Motifs; D000094704:RNA, Guide, CRISPR-Cas Systems / Q000138:chemical synthesis* / Q000235:genetics; D012984:Software
chemical_list: D001426:Bacterial Proteins; D000094704:RNA, Guide, CRISPR-Cas Systems; D000076987:CRISPR-Associated Protein 9; C000606107:Cas9 endonuclease Streptococcus pyogenes; D004720:Endonucleases