StructAnalyzer - a tool for sequence vs. structure similarity analysis

Abstract

In the world of RNAs and proteins similarities on the level of primary structures of two comparable molecules usually correspond to structural similarities on the tertiary level. In other words, measures of sequence and structure similarities are in general correlated – high value of sequence similarity impose high value of structural similarity. However important exceptions  that stay in contrary with the general rule can be identified. It is possible to find similar structures with very different sequences and also similar sequences with very different structures. In this paper we focus attention on the latter case and propose  a tool, called StructAnalyzer, supporting analysis of relations between sequence and structure similarities. Recognition of diversity of tertiary structures of molecules with very similar primary structures may be the key for better understanding of mechanisms influencing folding of RNA or proteins and as result their function. StructAnalyzer allows exploration and visualization of structural diversity in relation to sequence similarity. We show how the tool can be used to screen RNA structures in PDB for sequences with structural variants.