ScanFold: an approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV.

ABSTRACT: In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are cons

SUBMITTER: Andrews RJ 

PROVIDER: S-EPMC6317755 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature