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Updated: Jun 25, 2026

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
Published on: July 21, 2014
Performance evaluation of DNA motif discovery programs
Chandra Prakash Singh1, Feroz Khan, Bhartendu Nath Mishra
1Department of Computer Sciences, R.S.M.T., U.P. College, Varanasi, India. chand_11_2000@yahoo.com
Abstract:
Methods for the identification of transcription factor binding sites have proved to be useful for deciphering genetic regulatory networks. The strengths and weaknesses for a number of available web tools are not fully understood. Here, we designed a comprehensive set of performance measures and benchmarked sequence-based motif discovery tools using large scale datasets (derived from Escherichia coli genome and RegulonDB database). The benchmark study showed that nucleotide based and binding site based prediction accuracy is often low and activator binding site based prediction accuracy is high.
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