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In Genomics

Identification of microRNAs from plants is a crucial step for understanding the mechanisms of pathways and regulation of genes. A number of tools have been developed for the detection of microRNAs from small RNA-seq data. However, there is a lack of a pipeline for detection of miRNA from EST dataset even when a huge resource is publicly available and the method is known. Here we present, miRDetect a python implementation to detect novel miRNA precursors from plant EST data using homology and machine learning approach. 10-fold cross validation was applied to choose best classifier based on ROC, accuracy, MCC and F1-scores using 112 features. miRDetect achieved a classification accuracy of 93.35% on a Random Forest classifier and outperformed other precursor detection tools in terms of performance. The miRDetect pipeline aids in identifying novel plant precursors using a mixed approach and will be helpful to researchers with less informatics background.

Ayachit Garima, Pandya Himanshu, Das Jayashankar

2020-May-04

EST, Machine learning, Novel precursor, Pipeline, Plant, miRNA