A uniform projection method for motif discovery in DNA sequences

Benjamin Raphael, Lung Tien Liu, George Varghese

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Buhler and Tompa introduced the random projection algorithm for the motif discovery problem and demonstrated that this algorithm performs well on both simulated and biological samples. We describe a modification of the random projection algorithm, called the uniform projection algorithm, which utilizes a different choice of projections. We replace the random selection of projections by a greedy heuristic that approximately equalizes the coverage of the projections. We show that this change in selection of projections leads to improved performance on motif discovery problems. Furthermore, the uniform projection algorithm is directly applicable to other problems where the random projection algorithm has been used, including comparison of protein sequence databases.

Original languageEnglish (US)
Pages (from-to)91-94
Number of pages4
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Issue number2
StatePublished - Apr 2004
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Applied Mathematics
  • Genetics
  • Biotechnology


  • Combinatorial designs
  • Low-discrepancy sequences
  • Motif discovery
  • Random projection
  • Transcription factor binding sites


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