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Life Sciences Commons

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Faculty Publications

Bioinformatics

2005

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Full-Text Articles in Life Sciences

Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara Jan 2005

Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara

Faculty Publications

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy ...