In silico identification of novel endo-siRNAs

Many classes of small noncoding RNAs (sncRNAs), such as microRNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs), have been identified as important regulators of gene expression. Endo-siRNAs represent an integral part of the endogenous RNAi pathway and have been identified in multiple organisms and cell types. Wide adoption of the next-generation deep sequencing (NGS)-based sncRNA profiling has made the identification of novel sncRNA species more accessible. However, it remains a challenge to identify novel endo-siRNAs that are not collected in the current endo-siRNA databases. We have developed an in silico method for identification of novel endo-siRNAs using small RNA NGS data. Here, we describe our protocol in detail.