Title

Performance Evaluation of DNA MOTIF discovery programs

Authors

Chandra Prakash Singh^1*, Feroz Khan², Bhartendu Nath Mishra³, Durg Singh Chauhan⁴

Affiliation

¹Department of Computer Sciences, R.S.M.T., U.P. College, Varanasi, India; ²Bioinformatics Division, C.I.M.A.P. (C.S.I.R.), Lucknow, India; ³Department of Biotechnology, I.E.T., U.P. Technical University, Lucknow, India; ⁴Institute of Technology, B.H.U., Varanasi, India

Email

chand_11_2000@yahoo.com; * Corresponding author

Article Type

Hypothesis

Date

received November 11, 2008; accepted December 01, 2008; published December 31, 2008

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.

Keywords

 regulatory proteins; DNA binding site; motif discovery; accuracy; evaluation

Citation

Singh et al., Bioinformation 3(5): 205-212 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.