Abstract
The promoter is a regulatory region of the DNA typically located upstream of a gene and plays a key role in regulating gene transcription. Accurate prediction of promoters is crucial for the analysis of gene expression patterns and for the development and understanding of genetic regulatory networks. Genomes of several species have been sequenced, and their gene content has been established to a large extent. Some bioinformatics algorithms have been developed for predicting promoters with high universality for all kinds of plants; however, few studies have been conducted to identify promoters in rice, which might affect the practical applications. Here, we present a rice promoter prediction tool, Cr-Prom. This predictor has been established using a series of sequence-based features and datasets extracted from the PlantProm and RAP-DB databases. We applied a convolutional neural network (CNN)-based strategy to construct a predictor with robust classification performance. To demonstrate our dominance, we ran experiments on a benchmark dataset using 5-fold cross-validation and compared our results with existing techniques using four figure of merits. In addition, CR-Prom was analyzed on an independent dataset. Based on the results, Cr-Prom outperformed the existing rice-specific promoter predictors. The Cr-Prom tool can be freely accessed at: http://nsclbio.jbnu.ac.kr/tools/Cr-Prom/
Highlights
Rice is a cereal crop that belongs to the Orayza genus, representing a variety of rice, which can be divided into two subspecies, namely indica and japonica
The one-hot encoding scheme shows great effectiveness when applied in deep learning; a number of recent studies in the domain of computer science [27]–[29] and bioinformatics [30]–[32] have applied the one-hot encoding scheme
Numerous notable examples use convolutional neural network (CNN) to build predictors that can detect the variation occurred in genetic sequence
Summary
Rice is a cereal crop that belongs to the Orayza genus, representing a variety of rice, which can be divided into two subspecies, namely indica and japonica. Rice can be divided into conventional and hybrid rice depending upon its production type. Being a vital direct cash crop, rice is the staple food for majority of the population all over the world. From basic studies to molecular breeding, researchers have played a significant role in boosting rice production worldwide. Owing to the rapid development of biotechnology and genetic engineering technology, scientists started analyzing and collating rice genome in 1998, and by 2002, the entire rice genome map had been interpreted.
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