StructMiner: a tool for alignment and detection of conserved secondary structure.

Functional RNA molecules typically have structural patterns that are highly conserved in evolution. Here we present an algorithmic method for multiple alignment of RNAs, taking into consideration both structural similarity and sequence identity. Furthermore, our window-sized comparative analysis corrects the misaligned structure within a distance threshold and identifies the conserved substructures. Based on this new algorithm, StructMiner outperforms existing approaches, which ignore structure information for the alignment and lack the effective means to adjust the misalignments in the analysis phase. In addition, StructMiner is efficient in terms of CPU time and memory usage, making it suitable for structural analysis of very long sequences.