FindBacksplice: a Tool for Locating Circular RNA Backsplice Coordinates

Abstract

Circular RNAs (circRNAs) are generated through back-splicing, a process where a backsplice junction (BSJ) is formed, based on the circRNAs unique sequence. BSJs are highly conserved and can be mapped to chromosomal coordinates. Current platforms determine these coordinates from bulk RNA sequencing data. We aimed to develop a tool capable of determining backsplice coordinates based on BSJ sequences for any species and genome version. MotivationcircRNAs are emerging as an important regulator of cellular differentiation and other biologically important processes. Common tools for circRNA analyses require a circular RNAs backsplice coordinates. These can be accessed from public databases. However, the coordinates are specific to a version of a species genome, and are unavailable for many model organisms. ResultsWe have developed a Python-based, command line tool, FindBacksplice, which produces backsplice coordinates for any available genome, based on a circRNAs BSJ sequence. Implemented in Python, this script is integrated with BLAST for use in existing pipelines. We were able to find valid locations of backsplices for known human BSJs in the rat genome and produce backsplice coordinates for use in existing pipelines. Availability and implementationFindBacksplice is available at github.com/m-kraljevic/findbacksplice