A motif extraction algorithm based on hashing and modulo-4 arithmetic. (9th September 2008)

• Record Type: Journal Article
• Authors: Sheng, Huitao; Mehrotra, Kishan; Mohan, Chilukuri; Raina, Ramesh
• Is Part Of: International journal of computational biology and drug design. Volume 1:Number 2(2008)
• Page Start: 185
• Page End: 199
• Publication Date: 2008-09-09
• Subjects: cis-elements -- motif extraction -- gene expression -- gene regulation -- functional genomics -- coregulated genes -- simulation -- hashing -- motif discovery; Computational biology -- Periodicals; Drugs -- Design -- Periodicals; 570.285
• Languages: English
• ISSNs: 1756-0756

Abstract

We develop an algorithm to identify cis-elements in promoter regions of coregulated genes. This algorithm searches for subsequences of desired length whose frequency of occurrence is relatively high, while accounting for slightly perturbed variants using hash table and modulo arithmetic. Motifs are evaluated using profile matrices and higher-order Markov background model. Simulation results show that our algorithm discovers more motifs present in the test sequences, when compared with two well-known motif-discovery tools (MDScan and AlignACE). The algorithm produces very promising results on real data set; the output of the algorithm contained many known motifs.