I develop novel algorithms for prediction and alignment for RNA tertiary structure. The RNA-align algorithm I developed is the first RNA 3D structure alignment program based on a truly size-independent structure similarity metric (TM-score_RNA). I developed rMSA, an automated pipeline for deep RNA multiple sequence alignment generation. I also developed CSSR, which is the first programs that can accurately assign RNA secondary structure to a coarse-grained 3D structure. Currently, I am developing US-align, a unified pipeline for 3D structure alignment of complex and monomeric RNAs and proteins and for template-based docking.