MIT iGEM 2017 Modelling Group Project
Model and analyze to produce the most effective gRNA sequence in the CRISPR-(d)Cas13a system
Language: Python
Package required: Selenium, urllib, bs4(beautiful soup), tqdm
other loaded packages included: sys, re, csv, timeit, random, ast
Citations:
GC content:
1.Tessa G. Montague, José M. Cruz, James A. Gagnon, George M. Church, Eivind Valen; CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 2014; 42 (W1): W401-W407. doi: 10.1093/nar/gku410
2.Wang, Tim et al. “Genetic Screens in Human Cells Using the CRISPR/Cas9 System.” Science (New York, N.Y.) 343.6166 (2014): 80–84. PMC. Web. 5 July 2017.
3.Tsai, Shengdar Q. et al. “GUIDE-Seq Enables Genome-Wide Profiling of off-Target Cleavage by CRISPR-Cas Nucleases.” Nature biotechnology 33.2 (2015): 187–197. PMC. Web. 5 July 2017.
RBPmap:
1.Inbal Paz, Idit Kosti, Manuel Ares, Jr, Melissa Cline, Yael Mandel-Gutfreund; RBPmap: a web server for mapping binding sites of RNA- binding proteins. Nucleic Acids Res 2014; 42 (W1): W361-W367. doi: 10.1093/nar/gku406
Nupack:
1.J. N. Zadeh, C. D. Steenberg, J. S. Bois, B. R. Wolfe, M. B. Pierce, A. R. Khan, R. M. Dirks, N. A. Pierce. NUPACK: analysis and design of nucleic acid systems. J Comput Chem, 32:170–173, 2011.