RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Algorithms for phylogenetic footprinting
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
On the closest string and substring problems
Journal of the ACM (JACM)
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
On the complexity of finding common approximate substrings
Theoretical Computer Science
Fast and Practical Algorithms for Planted (l, d) Motif Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
RISOTTO: fast extraction of motifs with mismatches
LATIN'06 Proceedings of the 7th Latin American conference on Theoretical Informatics
An improved voting algorithm for planted (l,d) motif search
Information Sciences: an International Journal
Parallel motif extraction from very long sequences
Proceedings of the 22nd ACM international conference on Conference on information & knowledge management
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The planted (l,d)-motif search problem is a mathematical abstraction of the DNA functional site discovery task. In this paper, we propose a heuristic algorithm that can find planted (l,d)-signals in a given set of DNA sequences. Evaluations on simulated data sets demonstrate that the proposed algorithm outperforms current widely used motif finding algorithms. We also report the results of experiments on real biological data sets.