TSSPlant: a new tool for prediction of plant Pol II promoters
| Autor: | Ilham A. Shahmuradov, Victor V. Solovyev, Ramzan Umarov |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0106 biological sciences
0301 basic medicine Sequence analysis Arabidopsis Gene Expression RNA polymerase II Computational biology Mutually exclusive events 01 natural sciences Genome 03 medical and health sciences Genetics Promoter Regions Genetic Selection (genetic algorithm) Plant Proteins biology Artificial neural network Promoter Oryza Sequence Analysis DNA Backpropagation 030104 developmental biology biology.protein Methods Online Neural Networks Computer RNA Polymerase II Transcription Initiation Site Genome Plant Software 010606 plant biology & botany |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 |
| Popis: | 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/. |
| Databáze: | OpenAIRE |
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