Algorithm For Scanning Protein Sequences To Identify Potential Prion-Like Regions
In collaboration with MIT and the University of Massachusetts Medical School, Alex created a scaled-up version of a Hidden Markov Model algorithm for searching protein sequences for potential prion-like, structured regions of proteins. This program, called PLAAC (for prion-like amino acid composition) can find and rank candidate prion-like proteins of interest over entire proteome.
This algorithm and extensions have since been used in many studies to identify and visualize prion-like sequences in yeast, human and plant proteomes. Bulk text output files can be downloaded for further analyses, and visualizations saved in multiple formats such as PDF and PNG. This project implemented a web-front end, and the entire software platform is available to scientists under the MIT License via GitHub.com.