CRISPy-web: An online resource to design sgRNAs for CRISPR applications

Synthetic and Systems Biotechnology

Volumn 1, Issue 2, 2016, Pages 118-121

  Blin, Kai ^a   Pedersen, Lasse Ebdrup ^a   Weber, Tilmann ^a   Lee, Sang Yup ^a,b  

^a Chalmers University of Technology   (Denmark)

^b Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

Cas9; CRISPR; Genome editing; Genome engineering; Guide RNA; SgRNA

Indexed keywords

ACTINORHODINE;

ADAPTIVE IMMUNITY; ARTICLE; CRISPR CAS SYSTEM; GENE CLUSTER; GENE TARGETING; GENETIC ENGINEERING; NONHUMAN; ONLINE SYSTEM; PROCESS DESIGN; STREPTOCOCCUS PYOGENES; STREPTOMYCES COELICOLOR; WEB BROWSER;

EID: 84983290764     PISSN: None     EISSN: 2405805X     Source Type: Journal    
DOI: 10.1016/j.synbio.2016.01.003     Document Type: Article

References (26)

1. Horvath P., Barrangou R. CRISPR/Cas, the immune system of Bacteria and Archaea. Science 2010, 327:167-170.
2. Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014, 346. 1258096.
3. Jiang W., Bikard D., Cox D., Zhang F., Marraffini L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 2013, 31:233-239.
4. Tong Y., Charusanti P., Zhang L., Weber T., Lee S.Y. CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 2015, 4:1020-1029.
5. Cobb R.E., Wang Y., Zhao H. High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 2015, 4:723-728.
6. Ronda C., Maury J., Jakociunas T., Jacobsen S.A., Germann S.M., Harrison S.J., et al. CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae. Microb Cell Fact 2015, 14:97.
7. Jakociunas T., Bonde I., Herrgard M., Harrison S.J., Kristensen M., Pedersen L.E., et al. Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab Eng 2015, 28:213-222.
8. Shan Q., Wang Y., Li J., Zhang Y., Chen K., Liang Z., et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 2013, 31:686-688.
9. Shalem O., Sanjana N.E., Hartenian E., Shi X., Scott D.A., Mikkelsen T.S., et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 2014, 343:84-87.
10. Zetsche B., Gootenberg J.S., Abudayyeh O.O., Slaymaker I.M., Makarova K.S., Essletzbichler P., et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 2015, 163(3):759-771.
11. Esvelt K.M., Mali P., Braff J.L., Moosburner M., Yaung S.J., Church G.M. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 2013, 10:1116-1121.
12. Friedland A.E., Baral R., Singhal P., Loveluck K., Shen S., Sanchez M., et al. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol 2015, 16:257.
13. Shmakov S., Abudayyeh O.O., Makarova K.S., Wolf Y.I., Gootenberg J.S., Semenova E., et al. Discovery and functional characterization of diverse class 2 CRISPR-cas systems. Mol Cell 2015, 60:385-397.
14. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
15. Stemmer M., Thumberger T., Del Sol Keyer M., Wittbrodt J., Mateo J.L. CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS ONE 2015, 10:e0124633.
16. Montague T.G., Cruz J.M., Gagnon J.A., Church G.M., Valen E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 2014, 42:W401-7.
17. Hsu P.D., Scott D.A., Weinstein J.A., Ran F.A., Konermann S., Agarwala V., et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013, 31:827-832.
18. Wong N., Liu W., Wang X. WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol 2015, 10.1101/026971.
19. Hodgkins A., Farne A., Perera S., Grego T., Parry-Smith D.J., Skarnes W.C., et al. WGE: a CRISPR database for genome engineering. Bioinformatics 2015, 31:3078-3080.
20. Ronda C., Pedersen L.E., Hansen H.G., Kallehauge T.B., Betenbaugh M.J., Nielsen A.T., et al. Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool. Biotechnol Bioeng 2014, 111:1604-1616.
21. Xie S., Shen B., Zhang C., Huang X., Zhang Y. sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS ONE 2014, 9:e100448.
22. Weber T., Blin K., Duddela S., Krug D., Kim H.U., Bruccoleri R., et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 2015, 43:W237-43.
23. Blin K., Medema M.H., Kazempour D., Fischbach M., Breitling R., Takano E., et al. antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 2013, 41:W204-12.
24. Medema M.H., Blin K., Cimermancic P., de Jager V., Zakrzewski P., Fischbach M.A., et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011, 39:W339-46.
25. Cock P.J., Antao T., Chang J.T., Chapman B.A., Cox C.J., Dalke A., et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009, 25:1422-1423.
26. Fielding R.T., Taylor R.N. Principled design of the modern Web architecture. ACM T Internet Techn 2002, 2:115-150.