Crispy Public

CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing. This tool focuses on generating guide RNA sequences for Yeast and Bacterial species used in bioenergy research. This tool supports a 1011 genome Saccharomyces cerevisiae strain set as well as a 167 strain set of S. cerevisiae isolates

This application is currently hosted by the Great Lakes Bioenergy Research Center here: https://crispy-pop.glbrc.org/

The search by gene feature requires ~7 GB of reference data. If you would like access to this data, please contact us at contact email

app-specific prereqs

ruby / rails
sqlite3
yarn
python3
pip

python/pip prereqs

biopython
gffutils
numpy
scipy
scikit-learn

open source tools

samtools (1.5)
bcftools (1.5)
intel opencl runtime (16.1.1)
cas-offinder (2.4)
ncbi-blast (2.7.1+) -- for: blastn

environment variables:

export RAILS_ENV=production
export crispy_DATABASE=crispy
export crispy_USERNAME=crispy
export crispy_PASSWORD=[in-keepass]

Setup Instructions

1. install all dependencies
2. clone repository (cd to app directory)
3. create settings.yml and database.yml files in config/ based on the sample files threre
4. bundle install
5. yarn install
6. rails db:migrate
7. rails db:seed
8. rails server

CRISpy-pop utilizes the following open-source software tools:

Cas-OFFinder

Bae S., Park J. & Kim J.-S. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475 (2014).

sgRNA Scorer

Chari R, Yeo N, Chavez A, Church GM (2017). sgRNA Scorer 2.0 – a species independent model to predict CRISPR/Cas9 activity. ACS Synthetic Biology. Accepted.

CasFinder

Aach J, Mali P, Church GM (2014). CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. BioRxiv.

Contact Info

Please contact us at contact email with bugs or feature requests