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Gene Slider: sequence logo interactive data-visualization for education and research.

Jamie Waese1, Asher Pasha1, Ting Ting Wang1

  • 1Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada.

Bioinformatics (Oxford, England)
|August 14, 2016
PubMed
Summary
This summary is machine-generated.

Gene Slider is a tool for visualizing DNA and protein sequence conservation and entropy. It aids in identifying conserved non-coding regions and transcription factor binding sites in plants.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Understanding sequence conservation and regulatory elements is crucial for deciphering gene function.
  • Visualizing large-scale genomic data, including conserved non-coding regions and transcription factor binding sites, presents a significant challenge.

Purpose of the Study:

  • To develop and present Gene Slider, a novel tool for visualizing sequence conservation and entropy.
  • To enable the identification of cis-elements and transcription factor binding sites within conserved regions.
  • To provide a user-friendly interface for exploring genomic data, particularly conserved non-coding regions in Brassicaceae.

Main Methods:

  • Gene Slider employs sequence logos for visualizing conservation and entropy across orthologous DNA and protein sequences.
  • A search function allows motif discovery by 'drawing' sequence logo queries.
  • The tool integrates a database of conserved non-coding regions in Brassicaceae, indexed to Arabidopsis thaliana (TAIR10).

Main Results:

  • Gene Slider provides interactive visualization, allowing users to zoom from whole sequences to specific residues.
  • The tool successfully displays a large database of conserved non-coding regions and associated transcription factor binding sites.
  • It facilitates the identification of regions that are both evolutionarily conserved and potentially functionally relevant due to transcription factor binding.

Conclusions:

  • Gene Slider offers an effective platform for exploring sequence conservation and identifying potential regulatory elements.
  • The tool's visualization capabilities enhance the discovery of functionally important genomic regions.
  • Gene Slider is freely available and supports cross-browser compatibility, promoting its accessibility in biological research.