Mining metagenomes for new CRISPR effectors

This is a Python pipeline and CLI for identifying novel orthologs of CRISPR-Cas effectors from publicly available metagenome data.

Given a set of known protein sequences, it:

1. queries local metagenomic BLAST databases for similar ORFs using TBLASTN 🧬
2. searches significant contigs for putative CRISPR arrays using CRISPRFinder¹ 🔍
3. ranks, cleans, and summarizes the results for subsequent synthesis and experimental characterization. 🧪

In addition, it includes helper functions for:

• sorting, formatting, and preprocessing raw sequence data into searchable BLAST databases
• efficiently deduplicating sequences
• multithreading
• logging output
• basic job scheduling, including customizable SMS alerts whenever a run finishes or fails.

Developed during my Summer 2019 research in the Hsu Lab at the Salk Institute.

References

1. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. (2007):W52-7. https://doi.org/10.1093/nar/gkm360 ↩