Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures.

ABSTRACT:

Motivation

Non-canonical (or non-B) DNA are genomic regions whose three-dimensional conformation deviates from the canonical double helix. Non-B DNA play an important role in basic cellular processes and are associated with genomic instability, gene regulation, and oncogenesis. Experimental methods are low-throughput and can detect only a limited set of non-B DNA structures, while computational methods rely on non-B DNA base motifs, which are necessary but not sufficient indicators of non-B structures. Oxford Nanopore sequencing is an efficient and low-cost platform, but it is currently unknown whether nanopore reads can be used for identifying non-B structures.

Results

We build the first computational pipeline to predict non-B DNA structures from nanopore sequencing. We for

SUBMITTER: Hosseini M 

PROVIDER: S-EPMC10311326 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature