Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures.

ABSTRACT: The characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts. We present a graph convolutional network-based deep learning framework for predicting kmer characteristic ionic currents from corresponding chemical structures. We show such a framework can generalize the chemical information of the 5-methyl group from thymine to cytosine by correctly predicting 5-methylcytosine-containing DNA 6mers, thus shedding light on the de novo detection of nucleotide modifications.

SUBMITTER: Ding H 

PROVIDER: S-EPMC8586022 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature