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Microtubule Associated Proteins (MAPs)01:42

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Related Experiment Video

Updated: Jul 1, 2026

Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope Using the Tile/SED/Array Interface
06:15

Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope Using the Tile/SED/Array Interface

Published on: September 15, 2023

MTAP: the motif tool assessment platform.

Daniel Quest1, Kathryn Dempsey, Mohammad Shafiullah

  • 1College of Information Science & Technology, University of Nebraska at Omaha, Omaha NE, USA. djquest@unmc.edu

BMC Bioinformatics
|September 20, 2008
PubMed
Summary
This summary is machine-generated.

Assessing de novo regulatory motif discovery software is challenging. We developed MTAP, a method that automates tool pipelines and provides benchmarks, significantly reducing manual effort for researchers.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • De novo regulatory motif discovery is crucial for understanding gene regulation.
  • Over 150 software tools exist, making selection difficult due to performance variability.
  • Labs often invest significant manual effort in testing these tools.

Purpose of the Study:

  • To reduce the effort required to assess de novo regulatory motif discovery software.
  • To provide a standardized and automated benchmarking approach for motif discovery tools.

Main Methods:

  • Developed a novel method, MTAP (Motif Tool Assessment Pipeline).
  • Automated the construction of regulatory motif discovery tool pipelines.
  • Automated the generation of orthologous upstream sequences for benchmarking.
  • Provided automated benchmarks for popular motif discovery tools.

Main Results:

  • MTAP substantially reduces the manual effort in assessing motif discovery software.
  • Proof-of-concept benchmarks were successfully run across multiple species (human, mouse, fly, yeast, E. coli, B. subtilis).

Conclusions:

  • MTAP offers a new, automated approach to the assessment of regulatory motif discovery methods.
  • The developed method simplifies the process of identifying optimal tools for specific research needs.