FragmentFinder—a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA

Noncoding RNAs <200 nucleotides (nt) in length are referred to as short noncoding RNAs (sncRNAs) and include microRNAs (miRNAs), piwi-interacting RNAs, small nucleolar RNAs, transfer RNAs, etc. One striking example of the regulatory capabilities of sncRNAs comes from a group of small yet potent RNAs called miRNAs. MiRNAs are ∼20-nt RNAs excised from longer pre-miRNA hairpins, and to date, thousands of miRNAs have been identified across an array of species with specific roles for miRNAs defined in virtually every cellular activity (e.g. growth, differentiation, apoptosis, and disease). Importantly, studies aimed at evaluating the transcriptomic changes of miRNAs have now revealed the existence of miRNA-like fragments derived from other types of sncRNAs and suggest similar regulatory capacities may be associated with these novel sncRNA fragments. Unfortunately, many biologically relevant sncRNA-excised fragments remain uncharacterized due to their routine exclusion during initial miRNA characterizations as "sncRNA degradation products" as well as nearly all sncRNA informatic analyses continuing to solely assess annotated miRNA expressions. To address this, several platforms aimed at identifying novel sncRNA fragments have recently been developed. That said, the principal analytical tools currently employed to characterize novel sncRNA fragments often require significant computational expertise hindering their widespread utilization. As such, the development of a user-friendly platform, requiring minimal programming experience yet capable of identifying and characterizing RNA fragments excised from any sncRNA from any species is highly desirable and potentially impactful. In light of this, we have developed FragmentFinder-an intuitive, Windows-executable resource designed to require absolutely no computational background and capable of accurately characterizing all (annotated and unknown) sncRNA-derived RNAs within a raw small RNA sequencing file in real time.