title: TSSPlant: a new tool for prediction of plant Pol II promoters.
abstract: 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≃0.84 and F1-score≃0.91 versus MCC≃0.51 and F1-score≃0.71) and TATA-less promoters (MCC≃0.80, F1-score≃0.89 versus MCC≃0.29 and F1-score≃0.50). TSSPlant is available to download as a standalone program at http://www.cbrc.kaust.edu.sa/download/.
authors.affiliation: King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.|Institue of Molecular Biology and Biotechnologies, ANAS, 2 Matbuat strasse, Baku AZ1073, Azerbaijan.
authors.forename: Ilham A
authors.initials: IA
authors.lastname: Shahmuradov
authors.affiliation: King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
authors.forename: Ramzan Kh
authors.initials: RK
authors.lastname: Umarov
authors.affiliation: Softberry Inc., Mount Kisco, NY 10549, USA.
authors.forename: Victor V
authors.initials: VV
authors.lastname: Solovyev
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D018745:Genome, Plant; D016571:Neural Networks, Computer; D012275:Oryza / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012984:Software; D024363:Transcription Initiation Site
chemical_list: D010940:Plant Proteins; D012319:RNA Polymerase II