Congratulation to our Platform 5 Co-Lead Dr. Fiona Brinkman on this recent publication!
Abstract
We report PSORTm, the first bioinformatic tool designed for prediction of diverse bacterial and archaeal protein subcellular lo from metagenomics data. PSORTm incorporates components of PSORTb, one of the most precise and widely used protein SCL predictors, with an automated classification by cell envelope. An evaluation using 5-fold cross validation with in silico fragmented sequences with known localization showed that PSORTm maintains PSORTb’s high precision, while sensitivity increases proportionately with metagenomic sequence fragment length. PSORTm’s read-based analysis was similar to PSORTb-based analysis of metagenome-assembled genomes (MAGs), however the latter requires non-trivial manual classification of each MAG by cell envelope, and cannot make use of unassembled sequences. Analysis of the watershed samples revealed the importance of normalization and identified potential biomarkers of water quality. This method should be useful for examining a wide range of microbial communities, including human microbiomes, and other microbiomes of medical, environmental, or industrial importance.
Publication: PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data. Peabody MA, Lau VWY, Hoad GR, Jia B, Maguire F, Gray KL, Beiko RG, Brinkman FSL. Bioinformatics. 1 May 2020.
