NCM 2022: Developing new bioinformatics methods to identify modifications from nanopore sequencing

There are microbes everywhere and they play an important role in almost every aspect of life. To gain a deeper understanding of these organisms, it is necessary to identify epigenetic modifications, as understanding the epigenome enables both functional analysis and manipulation. Modification diversity and sequence context also differentiate microbes and provide an additional dimension of resolution to metagenomic analyses.
Nanopore sequencing is a readily available sequencing platform that has the potential to detect DNA modifications. The majority of current tools rely on pretrained models to predict the presence of modified motifs, limiting the detection of DNA modifications to already known types. In order to uncover novel modifications and use them in metagenomic studies, it is necessary to develop new methods to identify the full spectrum of modifications and motifs.
Here, we explore de novo identification of modification motifs using a comparison-based approach. This approach allows identification of modified motifs without any prior knowledge.