Infectious Diseases - Tools
A new tool for large-scale reverse vaccinology
I have a long track record of developing computational and analytical approaches to support translational efforts aimed at developing new vaccines and therapeutics. In collaboration with the team of Dr. Rino Rappuoli at GlaxoSmithKline (former Chiron Vaccines and Novartis Vaccines and Diagnostics), I leveraged bacterial genome information to pioneer the Reverse Vaccinology approach that identifies and prioritizes novel vaccine candidates using whole genome sequencing. We recently developed an updated reverse vaccine ology pipeline, ReVac, that implements both a panoply of feature prediction programs without filtering out proteins, and scoring of candidates based on predictions made on curated positive and negative control protein datasets. ReVac surveys several genomes assessing protein conservation, as well as DNA and protein repeats, which may result in variable expression of potential vaccine candidates (PVCs). ReVac’s orthologous clustering of conserved genes, identifies core and dispensable genome components. ReVac’s use of a scoring scheme ranks PVCs for subsequent experimental testing. Application of ReVac to two COPD pathogens prioritized PVCs, identifying both novel and previously validated PVCs.
[PI: Hervé Tettelin; collaborator Tim Murphy, U. at Buffalo]
TwinBLAST was developed to allow for easy visual inspection of two BLAST reports simultaneously.
LGTSeek can be used to detect the recent integration of DNA from paired end Illumina data with some knowledge about the donor and/or recipient genome.