The interactions of genes across species in a microbiome play a key role in shaping our ecosystems. Understanding and controlling microbiomes at the genetic level represents an emerging front in managing our health, food, energy, and the environment. Rapid development and application of state-of-the-art analytical tools has generated a large volume of omics data, expanding our understanding of these complex biological systems at the molecular level. To leverage such a rich data set, we developed a first-in-kind computational software tool for interrogating microbiomes using CRISPR-Cas gene editing technologies. Our
CRISPR
Associated
Software for
Pathway
Engineering and
Research (CASPER) enables gRNA generation and analysis in any organism or metagenome with any CRISPR-Cas system
1,2. CASPER combines traditional gRNA design tools (on- and off-target prediction, gRNA visualization, etc.) with unique functions such as multiple Cas-type gRNA generation and evaluation of spacer redundancy in a single species or microbiome. The analyses have implications for strain-, species-specific, or genus-specific CRISPR diagnostic probe design and microbiome manipulation. The novel features of CASPER are packaged in a user-friendly interface to create a computational environment for users to leverage the utility of CRISPR-Cas systems in their research. CASPER can be run on all major operating systems and is freely available for download at
https://github.com/TrinhLab/casperapp.
