PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

TLDR

PSORTb has been the most precise bacterial protein subcellular localization predictor since 2003. The authors aimed to improve recall, extend predictions to archaea, distinguish key subcategories, and provide a freely available web‑based and standalone tool. They benchmarked PSORTb against other predictors using 5‑fold cross‑validation and an independent proteomics analysis, and added a batch results delivery system to the web interface. PSORTb 3.0 delivers higher recall, broader proteome‑scale coverage, refined localization subcategories, and is the first predictor for all prokaryotes, including archaea and bacteria with atypical membrane/cell‑wall topologies, with an improved standalone program. The software and web interface are available at http://www.psort.org/psortb, with contact psort‑[e-mail] and supplementary data online.

Abstract

Abstract Motivation: PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program. Results: We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions. Availability: http://www.psort.org/psortb (download open source software or use the web interface). Contact: [e-mail] Supplementary Information: Supplementary data are availableat Bioinformatics online.