title: StructAnalyzer - a tool for sequence versus structure similarity analysis.
abstract: In the world of RNAs and proteins, similarities at the level of primary structures of two comparable molecules usually correspond to structural similarities at the tertiary level. In other words, measures of sequence and structure similarities are in general correlated - a high value of sequence similarity imposes a high value of structural similarity. However, important exceptions that stay in contrast to this general rule can be identified. It is possible to find similar structures with very different sequences, as well as similar sequences with very different structures. In this paper, we focus our attention on the latter case and propose a tool, called StructAnalyzer, supporting analysis of relations between the sequence and structure similarities. Recognition of tertiary structure diversity of molecules with very similar primary structures may be the key for better understanding of mechanisms influencing folding of RNAs or proteins, and as a result for better understanding of their function. StructAnalyzer allows exploration and visualization of structural diversity in relation to sequence similarity. We show how this tool can be used to screen RNA structures in Protein Data Bank (PDB) for sequences with structural variants.
authors: Institute of Computing Science, Poznan University of Technology, Poznań, Poland.
authors: Jakub
authors: J
authors: Wiedemann
authors: Institute of Computing Science, Poznan University of Technology, Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
authors: Maciej
authors: M
authors: Miłostan
mesh_terms: D001483:Base Sequence; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D017421:Sequence Analysis; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D012313:RNA