CRISPR-Cas sytems: tools and data
- This website collects several computational tools that we developed for CRISPR identification in metagenomic sequences; and some results from the papers we published.
- Tools
- Web server
- Data
- Cas genes identified from the HMP datasets (see the datta) (paper: Ref 2)
- Contigs and their annotations from Ref 3 (get the data; please read the readme file in the package).
- References
- Ref 1: Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak and Yuzhen Ye. Diverse CRISPRs evolving in human microbiomes (PLoS Genetics 8(6): e1002441, 2012) (paper link)
- Ref 2: Quan Zhang, Thomas G. Doak and Yuzhen Ye. Expanding the catalog of cas genes with metagenomes. Nucleic Acids Research, 42(4): 2448-2459 (2014) (paper link)
- Ref 3: Yuzhen Ye and Quan Zhang. Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data. 22(7): p. 945-56 (2016) (paper link)
- Ref 4: Quan Zhang and Yuzhen Ye. Not all predicted CRISPR-Cas systems are equal: Isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics, 18:92, 2017 (paper link; companion webserver)
- Tony Lam and Yuzhen Ye, CRISPRs for strain tracking and their application to microbiota transplantation data analysis. The CRISPR journal, http://doi.org/10.1089/crispr.2018.0046 (2018) (paper; software)
- Tony J. Lam and Yuzhen Ye. Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes. BMC Genomics 20, 567, doi:10.1186/s12864-019-5922-8 (2019) (paper)
- Contact: Yuzhen Ye (yye@indiana.edu)