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2006•Journal of Bioinformatics and Computational BiologyRequires access

ALGORITHMS FOR CHALLENGING MOTIF PROBLEMS

Henry C. M. Leung, Francis Y. L. Chin

Open publisher page 15 citations

Abstract

Pevzner and Sze(19) have introduced the Planted (l,d)-Motif Problem to find similar patterns (motifs) in sequences which represent the promoter regions of co-regulated genes, where l is the length of the motif and d is the maximum Hamming distance around the similar patterns. Many algorithms have been developed to solve this motif problem. However, these algorithms either have long running times or do not guarantee the motif can be found. In this paper, we introduce new algorithms to solve this motif problem. Our algorithms can find motifs in reasonable time for not only the challenging (9, 2), (11, 3), (15, 5)-motif problems but for even longer motifs, say (20, 7), (30, 11) and (40, 15), which have never been seriously attempted by other researchers because of the large time and space required. Besides, our algorithms can be extended to find more complicated motifs structure called cis-regulatory modules (CRM).

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What this paper is about

Pevzner and Sze(19) have introduced the Planted (l,d)-Motif Problem to find similar patterns (motifs) in sequences which represent the promoter regions of co-regulated genes, where l is the length of the motif and d is the maximum Hamming distance around the similar patterns. Many algorithms have been developed to solve this motif problem. However, these algorithms either have long running times or do not guarantee the motif can be found. In this paper, we introduce new algorithms to solve this motif problem. Our algorithms can find motifs in reasonable time for not only the challenging (9, 2), (11, 3), (15, 5)-motif problems but for even longer motifs, say (20, 7), (30, 11) and (40, 15), which have never been seriously attempted by other researchers because of the large time and space required. Besides, our algorithms can be extended to find more complicated motifs structure called cis-regulatory modules (CRM).

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OpenAlex reports 15 citations for this work. Citation counts describe recorded attention and do not establish research quality.

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Available abstract

Pevzner and Sze(19) have introduced the Planted (l,d)-Motif Problem to find similar patterns (motifs) in sequences which represent the promoter regions of co-regulated genes, where l is the length of the motif and d is the maximum Hamming distance around the similar patterns. Many algorithms have been developed to solve this motif problem. However, these algorithms either have long running times or do not guarantee the motif can be found. In this paper, we introduce new algorithms to solve this motif problem. Our algorithms can find motifs in reasonable time for not only the challenging (9, 2), (11, 3), (15, 5)-motif problems but for even longer motifs, say (20, 7), (30, 11) and (40, 15), which have never been seriously attempted by other researchers because of the large time and space required. Besides, our algorithms can be extended to find more complicated motifs structure called cis-regulatory modules (CRM).

Key concepts: Motif (music), Structural motif, Computer science, Hamming distance, Algorithm, Computational biology, Combinatorics, Mathematics

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