PENGUINN: Precise Exploration of Nuclear G-quadruplexes Using Interpretable Neural Networks

Abstract

G-quadruplexes (G4s) are a class of stable structural nucleic acid motifs that are known to play a role in a wide spectrum of genomic functions, such as DNA replication and transcription. The classical understanding of G4 structure points to four variable length guanine strands joined by variable length stretches of other nucleotides. Experiments using G4 immunoprecipitation and sequencing experiments have produced a high number of highly probable G4 forming genomic sequences. The expense and technical difficulty of experimental techniques highlights the need for computational approaches of G4 identification. Here, we present PENGUINN, a machine learning method based on Convolutional Neural Networks, that learns the characteristics of G4 sequences and accurately predicts G4s outperforming the state-of-the-art. We provide both a standalone implementation of the trained model, and a web application that can be used to evaluate sequences for their G4 potential.