ArticleAlgorithms for molecular biology : AMB2006
SMOTIF: efficient structured pattern and profile motif search.
Article in Algorithms for molecular biology : AMB, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Active motif finder - a bio-tool based on mutational structures in DNA sequences.Journal of biomedical research · 2011Article
- Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2011Article
- ModuleOrganizer: detecting modules in families of transposable elements.BMC bioinformatics · 2010Article
- Protein sequences classification by means of feature extraction with substitution matrices.BMC bioinformatics · 2010Article
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Authors and funding
2 authors.
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Abstract
backgroundA structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps. The motif can either be represented as a pattern or a profile (also called positional weight matrix). We propose an efficient algorithm, called SMOTIF, to solve the structured motif search problem, i.e., given one or more sequences and a structured motif, SMOTIF searches the sequences for all occurrences of the motif. Potential applications include searching for long terminal repeat (LTR) retrotransposons and composite regulatory binding sites in DNA sequences.
resultsSMOTIF can search for both pattern and profile motifs, and it is efficient in terms of both time and space; it outperforms SMARTFINDER, a state-of-the-art algorithm for structured motif search. Experimental results show that SMOTIF is about 7 times faster and consumes 100 times less memory than SMARTFINDER. It can effectively search for LTR retrotransposons and is well suited to searching for motifs with long range gaps. It is also successful in finding potential composite transcription factor binding sites.
conclusionSMOTIF is a useful and efficient tool in searching for structured pattern and profile motifs. The algorithm is available as open-source at: http://www.cs.rpi.edu/~zaki/software/sMotif/.
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