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

ABSTRACT:

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 sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently in

SUBMITTER: Meyer F 

PROVIDER: S-EPMC3154205 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature