Structator: fast index-based search for RNA sequence-structure patterns

Background: The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results: We present a novel method and readily applicable software for time efficient matching of RNA sequencestructure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Struct...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette
• Keywords: Biometrics, BMCBI 2011, RNA Molecules, Suffix Trees, Target Database