We present a large-scale benchmarking study of 17 state-of-the-art PPPs. A multi-faceted evaluation strategy is proposed that can be used as a gold standard for promoter prediction evaluation, allowing authors of promoter prediction software to compare their method to existing methods in a proper way. This evaluation strategy is subsequently used to compare the chosen promoter predictors, and an in-depth analysis on predictive performance, promoter class specificity, overlap between predictors and positional bias of the predictions is conducted.

Abeel, T., Van de Peer, Y., & Saeys, Y. (2009). Toward a gold standard for promoter prediction evaluation. BIOINFORMATICS, 25(12), I313–I320. Presented at the Joint conference of Intelligent Systems for Molecular Biology and the European conference on Computational Biology.