RibORF: Identifying Genome-Wide Translated Open Reading Frames Using Ribosome Profiling

Abstract

Ribosome profiling identifies RNA fragments associated with translating ribosomes. The technology provides an opportunity to examine genome-wide translation events at single-nucleotide resolution and in an unbiased manner. Here I present a computational pipeline named RibORF to systematically identify translated open reading frames (ORFs), based on read distribution features representing active translation, including 3-nt periodicity and uniformness across codons. Analyses using the computational tool revealed pervasive translation in putative ‘noncoding’ regions, such as lncRNAs, pseudogenes, and 5′UTRs. The computational tool is useful for studying functional roles of non-canonical translation events in various biological processes. © 2018 by John Wiley & Sons, Inc.