ArticleAlgorithms for molecular biology : AMB2006
EXMOTIF: efficient structured motif extraction.
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 7 papers.
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Who cites it
7 citing papers in PubMed.
- A Review on Planted (Sensors (Basel, Switzerland) · 2022Review
- libFLASM: a software library for fixed-length approximate string matching.BMC bioinformatics · 2016Article
- MoTeX-II: structured MoTif eXtraction from large-scale datasets.BMC bioinformatics · 2014Article
- Direct vs 2-stage approaches to structured motif finding.Algorithms for molecular biology : AMB · 2012Article
- Protein sequences classification by means of feature extraction with substitution matrices.BMC bioinformatics · 2010Article
- Data Mining in Bioinformatics (BIOKDD).Algorithms for molecular biology : AMB · 2007Article
- SMOTIF: efficient structured pattern and profile motif search.Algorithms for molecular biology : AMB · 2006Article
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Authors and funding
2 authors.
Funding
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Abstract
backgroundExtracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient algorithm, called EXMOTIF, that given some sequence(s), and a structured motif template, extracts all frequent structured motifs that have quorum q. Potential applications of our method include the extraction of single/composite regulatory binding sites in DNA sequences.
resultsEXMOTIF is efficient in terms of both time and space and is shown empirically to outperform RISO, a state-of-the-art algorithm. It is also successful in finding potential single/composite transcription factor binding sites.
conclusionEXMOTIF is a useful and efficient tool in discovering structured motifs, especially in DNA sequences. The algorithm is available as open-source at: http://www.cs.rpi.edu/~zaki/software/exMotif/.
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