Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible.

ABSTRACT:

Background

Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between r

SUBMITTER: McKerrow WH 

PROVIDER: S-EPMC5502491 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature