Identification of Secondary Structure Elements in miRNA using Signal Processing Method

Abstract

In the past, signal processing method has been applied on genomic data to reveal the periodicities that determine a wide variety of biological functions, ranging from exon detection to microsatellite identification. But, not much has been focused on RNA based signal processing. MicroRNAs (miRNA) are associated with gene regulation and gene silencing and thus have wide applications. The functionality of the miRNA is highly associated with its secondary structures (stem, bulge, and loop). Here, we show that signal processing method can be applied to miRNA sequences by implementing the Modified S-transform transform (MST) method to detect the periodicities between 2 and 11. We observed that these periodicities are highly correlated with the secondary structure of miRNA and possibly can be used as indicators of secondary and tertiary structure formation