Bidirectional search in a string with wavelet trees

Authors:
Thomas Schnattinger;Enno Ohlebusch;Simon Gog
Affiliations:
Institute of Theoretical Computer Science, University of Ulm, Ulm;Institute of Theoretical Computer Science, University of Ulm, Ulm;Institute of Theoretical Computer Science, University of Ulm, Ulm
Venue:
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Year:
2010

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Abstract

Searching for genes encoding microRNAs (miRNAs) is an important task in genome analysis. Because the secondary structure of miRNA (but not the sequence) is highly conserved, the genes encoding it can be determined by finding regions in a genomic DNA sequence that match the structure. It is known that algorithms using a bidirectional search on the DNA sequence for this task outperform algorithms based on unidirectional search. The data structures supporting a bidirectional search (affix trees and affix arrays), however, are rather complex and suffer from their large space consumption. Here, we present a new data structure called bidirectional wavelet index that supports bidirectional search with much less space. With this data structure, it is possible to search for RNA secondary structural patterns in large genomes, for example the human genome.