Deep and wide digging for binding motifs in ChIP-Seq data

I. V. Kulakovskiy, V. A. Boeva, A. V. Favorov, V. J. Makeev

Research output: Contribution to journalArticlepeer-review

99 Scopus citations


Summary: ChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of thousands of DNA segments with base-specific coverage values. We present a new version of our DNA motif discovery software ChIPMunk adapted for ChIP-Seq data. ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences. Comparison with traditional (MEME) or ChIP-Seq-oriented (HMS) motif discovery tools shows that ChIPMunk identifies the correct motifs with the same or better quality but works dramatically faster.

Original languageEnglish (US)
Article numberbtq488
Pages (from-to)2622-2623
Number of pages2
Issue number20
StatePublished - Oct 20 2010

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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