Optimal offline extraction of irredundant motif bases

Authors:
Alberto Apostolico;Claudia Tagliacollo
Affiliations:
Georgia Institute of Technology & Università di Padova;Georgia Institute of Technology & Università di Padova
Venue:
COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
Year:
2007

Citing 7
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Abstract

The problem of extracting a basis of irredundant motifs from a sequence is considered. In previous work such bases were built incrementally for all suffixes of the input string s in O(n3), where n is the length of s. Faster, non-incremental algorithms have been based on the landmark approach to string searching due to Fischer and Paterson, and exhibit respective time bounds of O(n2 log n log |Σ|) and O(|Σ|n2 log2 n log log n), with Σ denoting the alphabet. The algorithm by Fischer and Paterson makes crucial use of the FFT, which is impractical with long sequences. The algorithm presented in the present paper does not need to resort to the FFT and yet is asymptotically faster than previously available ones. Specifically, an off-line algorithm is presented taking time O(|Σ|n2), which is optimal for finite S.