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Related Experiment Videos

Locating potential enhancer elements by comparative genomics using the EEL software.

Kimmo Palin1, Jussi Taipale, Esko Ukkonen

  • 1Department of Computer Science, P.O. Box 68 (Gustaf Hällströmin katu 2b) FIN-00014, University of Helsinki, Finland. Kimmo.Palin@helsinki.fi

Nature Protocols
|April 5, 2007
PubMed
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Enhancer Element Locator (EEL) is a new software tool that identifies potential gene regulatory elements in DNA. This computational approach aids researchers in discovering enhancer locations and structures within mammalian genomes.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying distal enhancer elements is crucial for understanding gene regulation.
  • Mammalian genomes are complex, making enhancer discovery challenging.
  • Transcription factor binding specificities are key determinants of enhancer function.

Purpose of the Study:

  • To introduce Enhancer Element Locator (EEL), a novel computer program for identifying distal enhancer elements.
  • To describe the computational methodology employed by EEL for predicting enhancer location and structure.
  • To provide a freely available tool for researchers investigating gene regulation in mammalian DNA sequences.

Main Methods:

  • EEL utilizes two orthologous DNA sequences as input.
  • The program incorporates binding specificity matrices for relevant transcription factors (TFs).

Related Experiment Videos

  • EEL analyzes large DNA sequences (up to 1 Mb) and TF motifs computationally.

    • Main Results:

    • EEL successfully predicts the location and structure of conserved enhancers.
    • The software demonstrates efficiency, analyzing 1 Mb sequences with 100 TF motifs in approximately 15 minutes.
    • The output generates testable hypotheses regarding enhancer elements for expert evaluation.

    Conclusions:

    • EEL offers a powerful and efficient computational solution for discovering distal enhancer elements.
    • The software facilitates the exploration of enhancer function by providing predicted locations and structures.
    • EEL is a valuable, freely accessible resource for genomic research and the study of gene regulation.