Structural Biochemistry/Bioinformatics/Structural Alignments/RNA Structural Alignment

RNA Structural Alignment

Structural alignment techniques have traditionally only been applied to proteins, as they are the primary biological macromolecules that form characteristic three dimensional structures. However, large RNA molecules also form characteristic tertiary structures, which mostly consist of hydrogen bonds formed between base pairs as well as by base stacking. Functionally similar noncoding RNA molecules can be particularly difficult to extract from genomics data because structure is more strongly conserved than sequence in RNA as well as proteins, while the more limited alphabet of RNA decreases the information content of any given nucleotide at any given position. A recent method for pairwise structural alignment of RNA sequences with low sequence identity has been published and implemented in the program FOLDALIGN. This method is not truly analogous to protein structural alignment techniques because it computationally predicts the structure of the RNA input sequences rather than requiring experimentally determined structures as input. Although computational prediction of the protein folding process has not been particularly successful to date, RNA structures without pseudoknots can often be sensibly predicted using free energy-based scoring methods that account for base pairing and stacking.