SSFinder: High throughput CRISPR-Cas target sites prediction tool

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Upadhyay, Santosh Kumar ^a   Sharma, Shailesh ^a  

^a NATIONAL AGRI FOOD BIOTECHNOLOGY INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; NUCLEOTIDE;

ALGORITHM; ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPUTER PROGRAM; COMPUTER SYSTEM; CRISPR CAS SYSTEM; GENOME; HIGH THROUGHPUT SCREENING; MICROCOMPUTER; PREDICTION; SSFINDER; AUTOMATED PATTERN RECOGNITION; COMPUTER LANGUAGE; DNA SEQUENCE; GENE TARGETING; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES;

ALGORITHMS; BASE SEQUENCE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; GENE TARGETING; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PROGRAMMING LANGUAGES; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84904130263     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/742482     Document Type: Article

References (13)

1. Chen K., Gao C., TALENs: customizable molecular DNA scissors for genome engineering of plants. Journal of Genetics and Genomics 2013 40 6 271 279 10.1016/j.jgg.2013.03.009 2-s2.0-84879414846
2. Zhang F., Maeder M. L., Unger-Wallaced E., Hoshaw J. P., Reyon D., Christian M., Li X., Pierick C. J., Dobbs D., Peterson T., Joung J. K., Voytas D. F., High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proceedings of the National Academy of Sciences of the United States of America 2010 107 26 12028 12033 10.1073/pnas.0914991107 2-s2.0-77955395799
3. Cong L., Ran F. A., Cox D., Lin S., Barretto R., Habib N., Hsu P. D., Wu X., Jiang W., Marraffini L. A., Zhang F., Multiplex genome engineering using CRISPR/Cas systems. Science 2013 339 6121 819 823 10.1126/science.1231143 2-s2.0-84873729095
4. Mali P., Yang L., Esvelt K. M., Aach J., Guell M., DiCarlo J. E., Norville J. E., Church G. M., RNA-guided human genome engineering via Cas9. Science 2013 339 6121 823 826 10.1126/science.1232033 2-s2.0-84873734105
5. Upadhyay S. K., Kumar J., Alok A., Tuli R., RNA guided genome editing for multiple target gene mutations in wheat. G3: Genes, Genomes, Genetics 2013 3 12 2233 2238 10.1534/g3.113.008847
6. Jore M. M., Lundgren M., van Duijn E., Bultema J. B., Westra E. R., Waghmare S. P., Wiedenheft B., Pul Ü., Wurm R., Wagner R., Beijer M. R., Barendregt A., Zhou K., Snijders A. P. L., Dickman M. J., Doudna J. A., Boekema E. J., Heck A. J. R., Van Der Oost J., Brouns S. J. J., Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nature Structural & Molecular Biology 2011 18 5 529 536 10.1038/nsmb.2019 2-s2.0-79955574254
7. Gasiunas G., Barrangou R., Horvath P., Siksnys V., Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America 2012 109 39 E2579 E2586 10.1073/pnas.1208507109 2-s2.0-84866859751
8. Fu Y., Foden J. A., Khayter C., Maeder M. L., Reyon D., Joung J. K., Sander J. D., High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nature Biotechnology 2013 31 822 826 10.1038/nbt.2623
9. Li J. F., Norville J. E., Aach J., Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature Biotechnolog 2013 31 8 688 691 10.1038/nbt.2654
10. Qi L. S., Larson M. H., Gilbert L. A., Doudna J. A., Weissman J. S., Arkin A. P., Lim W. A., Repurposing CRISPR as an RNA- γ uided platform for sequence-specific control of gene expression. Cell 2013 152 5 1173 1183 10.1016/j.cell.2013.02.022 2-s2.0-84874687019
11. Bikard D., Jiang W., Samai P., Hochschild A., Zhang F., Marraffini L. A., Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Research 2013 41 15 7429 7437 10.1093/nar/gkt520
12. Biswas A., Gagnon J. N., Brouns S. J. J., Fineran P. C., Brown C. M., CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biology 2013 10 5 817 827 10.4161/rna.24046 2-s2.0-84879014174
13. Jinek M., East A., Cheng A., Lin S., Ma E., Doudna J., RNA-programmed genome editing in human cells. eLife 2013 2 e00471 10.7554/eLife.00471.001