Using Suffix Trees for Gapped Motif Discovery
- 413 Downloads
Gibbs sampling is a local search method that can be used to find novel motifs in a text string. In previous work , we have proposed a modified Gibbs sampler that can discover novel gapped motifs of varying lengths and occurrence rates in DNA or protein sequences. The Gibbs sampling method requires repeated searching of the text for the best match to a constantly evolving collection of aligned strings, and each search pass previously required θ(nl) time, where l is the length of the motif and n the length of the original sequence. This paper presents a novel method for using suffix trees to greatly improve the performance of the Gibbs sampling approach.
KeywordsTree Search Gibbs Sampling Edit Distance Suffix Tree Gibbs Sampling Algorithm
Unable to display preview. Download preview PDF.
- 1.Chang, W.I., Lampe, J., Theoretical and Empirical Comparisons of Approximate String Matching Algorithms. Proc. 3rd Symp. on Combinatorial Pattern Matching, Springer LNCS 644, 175–84, 1992.Google Scholar
- 5.Lawrence, Altschul, S., Boguski, M., Liu, J., Neuwald, A., Wootton, J. Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science, 262:208–214, 8 October 1993.Google Scholar
- 6.Marsan, L., Sagot, M.F., Extracting Structured Motifs Using a Suffix Tree—Algorithms and Application to Promoter Consensus Identification. To appear in Proceedings of RECOMB 2000.Google Scholar
- 8.Rocke, E., Tompa, M., An Algorithm for Finding Novel Gapped Motifs in DNA Sequences. Proceedings of the Second Annual International Conference on Computational Molecular Biology, 228–233., New York, NY, March 1998.Google Scholar
- 9.Sagot, M-F., Spelling Approximate Repeated or Common Motifs Using a Suffix Tree. Proceedings of LATIN, 374–390, 1998.Google Scholar
- 10.Smith, T.F., Waterman, M.S., Identification of Common Molecular Subsequences. J. Mol. Biol., 284:1–18, 1995.Google Scholar
- 11.Ukkonen, E., Approximate String-Matching Over Suffix Trees. Proc. 4th Symp. on Combinatorial Pattern Matching, Springer LCNS 684, 228–42, 1993.Google Scholar
- 14.Weiner, P., Linear Pattern Matching Algorithms. Proc. of the 14th IEEE Symp. on Switching and Automata Theory, 1–11, 1973.Google Scholar