MuStARD: a Deep Learning method for intra- and inter- species scanning identification of small RNA molecules
MuStARD: a Deep Learning method for intra- and inter- species scanning identification of small RNA molecules
ABSTRACT Genomic regions that encode small RNA genes exhibit characteristic patterns in their sequence, secondary structure, and evolutionary conservation. Deep Learning algorithms are efficient at classifying examples based on such learned patterns. Here we present MuStARD (gitlab.com/RBP_Bioinformatics/mustard) a Deep Learning framework that can learn patterns associated with user-defined sets of genomic regions, and scan large genomic areas for novel regions exhibiting similar characteristics. We demonstrate that MuStARD can be trained on different classes of human small RNA loci (pre-miRNAs and snoRNAs) and outperform state of the art methods specifically designed for each specific class. Furthermore, we demonstrate the ability of MuStARD for inter-species identification of functional elements by predicting mouse small RNAs (pre-miRNAs and snoRNAs) using models trained on the human genome. MuStARD is easy to deploy and extend to a variety of genomic classification questions.
Plessas Fotis C、Georgakilas Georgios K、Grioni Andrea、Malanikova Eliska、Liakos Konstantinos G、Alexiou Panagiotis
Department of Electrical and Computer Engineering, School of Engineering, University of ThessalyCentral European Institute of TechnologyCentral European Institute of Technology||Faculty of Science, National Centre for Biomolecular Research, Masaryk University||Centro Ricerca Tettamanti, Pediatric Department, University of Milano-BicoccaCentral European Institute of Technology||Faculty of Science, National Centre for Biomolecular Research, Masaryk UniversityDepartment of Electrical and Computer Engineering, School of Engineering, University of ThessalyCentral European Institute of Technology
分子生物学生物工程学计算技术、计算机技术
Plessas Fotis C,Georgakilas Georgios K,Grioni Andrea,Malanikova Eliska,Liakos Konstantinos G,Alexiou Panagiotis.MuStARD: a Deep Learning method for intra- and inter- species scanning identification of small RNA molecules[EB/OL].(2025-03-28)[2025-05-24].https://www.biorxiv.org/content/10.1101/547679.点此复制
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