title: Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.
abstract: This paper introduces two exact algorithms for extracting conserved structured motifs from a set of DNA sequences. Structured motifs may be described as an ordered collection of p > or = 1 "boxes" (each box corresponding to one part of the structured motif), p substitution rates (one for each box) and p - 1 intervals of distance (one for each pair of successive boxes in the collection). The contents of the boxes--that is, the motifs themselves--are unknown at the start of the algorithm. This is precisely what the algorithms are meant to find. A suffix tree is used for finding such motifs. The algorithms are efficient enough to be able to infer site consensi, such as, for instance, promoter sequences or regulatory sites, from a set of unaligned sequences corresponding to the noncoding regions upstream from all genes of a genome. In particular, both algorithms time complexity scales linearly with N2n where n is the average length of the sequences and N their number. An application to the identification of promoter and regulatory consensus sequences in bacterial genomes is shown.
authors: Institut Gaspard Monge, Université de Marne la Vallée 5.
authors: L
authors: L
authors: Marsan
authors: M F
authors: MF
authors: Sagot
mesh_terms: D000465:Algorithms; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D005809:Genes, Regulator; D016680:Genome, Bacterial; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*
chemical_list: D004269:DNA, Bacterial