Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

  • Zambelli F
  • Pesole G
  • Pavesi G
  • 6


    Mendeley users who have this article in their library.
  • N/A


    Citations of this article.


Motif discovery has been one of the most widely studied problems in bioinformatics ever since genomic and protein sequences have been available. In particular, its application to the de novo prediction of putative over-represented transcription factor binding sites in nucleotide sequences has been, and still is, one of the most challenging flavors of the problem. Recently, novel experimental techniques like chromatin immunoprecipitation (ChIP) have been introduced, permitting the genome-wide identification of protein-DNA interactions. ChIP, applied to transcription factors and coupled with genome tiling arrays (ChIP on Chip) or next-generation sequencing technologies (ChIP-Seq) has opened new avenues in research, as well as posed new challenges to bioinformaticians developing algorithms and methods for motif discovery.

Author-supplied keywords

  • *Regulatory Elements, Transcriptional
  • Algorithms
  • Animals
  • Binding Sites/genetics
  • Chromatin Immunoprecipitation/statistics & numeric
  • Computational Biology
  • Consensus Sequence
  • DNA/genetics/metabolism
  • Gene Expression Profiling/statistics & numerical d
  • High-Throughput Nucleotide Sequencing/*statistics
  • Humans
  • Transcription Factors/*metabolism

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document


  • F Zambelli

  • G Pesole

  • G Pavesi

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free