Promotech: a general tool for bacterial promoter recognition

Genome Biology

Ruben Chevez-Guardado¹  Lourdes Peña-Castillo² 

[1] Department of Computer Science, Memorial University of Newfoundland, 230 Elizabeth Ave, A1C 5S7, St. John’s, Newfoundland, Canada;Department of Computer Science, Memorial University of Newfoundland, 230 Elizabeth Ave, A1C 5S7, St. John’s, Newfoundland, Canada;Department of Biology, Memorial University of Newfoundland, 230 Elizabeth Ave, A1C 5S7, St. John’s, Newfoundland, Canada;

关键词: Bacterial promoter;    Promoter recognition;    Promoter prediction;    Machine learning;    Microbiology;    Bioinformatics;   

DOI  :  10.1186/s13059-021-02514-9

来源: Springer

【 摘 要 】

Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. However, most of these tools were designed to recognize promoters in one or few bacterial species. Here, we present Promotech, a machine-learning-based method for promoter recognition in a wide range of bacterial species. We compare Promotech’s performance with the performance of five other promoter prediction methods. Promotech outperforms these other programs in terms of area under the precision-recall curve (AUPRC) or precision at the same level of recall. Promotech is available at https://github.com/BioinformaticsLabAtMUN/PromoTech.

【 授权许可】

CC BY