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Algorithms for Molecular Biology BioMed Central Research Open Access Refining motifs by improving information content scores using neighborhood profile search Chandan K Reddy*, Yao-Chung Weng and Hsiao-Dong Chiang Address: School of Electrical and Computer Engineering, Cornell University, Ithaca, NY, 14853, USA Email: Chandan K Reddy* - ckr6@; Yao-Chung Weng - ycwweng@; Hsiao-Dong Chiang - chiang@ * Corresponding author Published: 27 November 2006 Received: 20 July 2006 Accepted: 27 November 2006 Algorithms for Molecular Biology 2006, 1:23 doi:10.1186/1748-7188-1-23 This article is available from: /content/1/1/23 © 2006 Reddy et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The main goal of the motif finding problem is to detect novel, over-represented unknown signals in a set of sequences (e.g. transcription factor binding sites in a genome). The most widely used algorithms for finding motifs obtain a generative probabilistic representation of these over- represented signals and try to discover profiles that maximize the information content score. Although these profiles form a very powerful representation of the signals, the major difficulty arises from the fact that the best motif corresponds to the global maximum of a non-convex continuous function. Popular algori