TSSPlant: a new tool for prediction of plant Pol II promoters

Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). Moreover, TSS selection depends on cell/tissue, development stage and environmental conditions. Such complex promoter structures make their computational identification notoriously difficult. Here, we present TSSPlant, a novel tool that predicts both TATA and TATA-less promoters in sequences of a wide spectrum of plant genomes. The tool was developed by using large promoter collections from ppdb and PlantProm DB. It utilizes eighteen significant compositional and signal features of plant promoter sequences selected in this study, that feed the artificial neural network-based model trained by the backpropagation algorithm. TSSPlant achieves significantly higher accuracy compared to the next best promoter prediction program for both TATA promoters (MCC similar or equal to 0.84 and F1-score similar or equal to 0.91 versus MCC similar or equal to 0.51 and F1-score similar or equal to 0.71) and TATA-less promoters (MCC similar or equal to 0.80, F1-score similar or equal to 0.89 versus MCC similar or equal to 0.29 and F1-score similar or equal to 0.50). TSSPlant is available to download as a standalone program at http://www.cbrc.kaust.edu.sa/download/.