A motif extraction algorithm based on hashing and modulo-4 arithmetic

Huitao Sheng, Kishan Mehrotra, Chilukuri Mohan, Ramesh Raina

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)185-199
Number of pages15
JournalInternational Journal of Computational Biology and Drug Design
Issue number2
StatePublished - 2008


  • cis-element
  • functional genomics
  • gene expression
  • gene regulation
  • motif

ASJC Scopus subject areas

  • Drug Discovery
  • Computer Science Applications


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