Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing

•NGS was applied to small RNA fractions with 40 to 140 nt.•Secondary structure-based clustering was performed.•16 candidate mouse structured small non-coding RNAs (MsncRs) were isolated.

In order to find novel structured small RNAs, next-generation sequencing was applied to small RNA fractions with lengths ranging from 40 to 140 nt and secondary structure-based clustering was performed. Sequences of structured RNAs were effectively clustered and analyzed by secondary structure. Although more than 99% of the obtained sequences were known RNAs, 16 candidate mouse structured small non-coding RNAs (MsncRs) were isolated. Based on these results, the merits of secondary structure-based analysis are discussed.