Computing Parametric Alignment of RNA Structures: Visualization and Practice

Alignment of RNA structures is very important in biological research. Similar to pair-wise sequence alignment, there is often disagreement about how to weight matches, mismatches, indels and gaps when comparing two RNA structures. Here, we develop a visual tool for computing parametric alignment of two RNA structures. With this tool, users can see explicitly and completely the effect of parameter choices on the optimal alignments of RNA structures. The software is available for academic use (http://www.cs.cityu.edu.hk/~lwang/software/ParaRNA/).