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DepLogo: visualizing sequence dependencies in R.

Jan Grau1, Martin Nettling1, Jens Keilwagen2

  • 1Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.

Bioinformatics (Oxford, England)
|June 22, 2019
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Summary
This summary is machine-generated.

The new DepLogo R package visualizes statistical dependencies in sequence data using dependency logos. This method makes complex sequence patterns, like those in DNA, RNA, and proteins, easier to see.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Statistical dependencies are crucial in sequence data analysis but are often missed by traditional methods like sequence logos.
  • Understanding inter-position dependencies is key to deciphering biological sequence functions.

Purpose of the Study:

  • To introduce the DepLogo R package for visualizing inter-position dependencies in aligned sequence data.
  • To enable visual perception of dependency structures and symbol co-occurrences.

Main Methods:

  • Developed the DepLogo R package for creating dependency logos.
  • Utilized mutual information to measure dependencies between sequence positions.
  • Partitioned sequences based on symbols at highly dependent positions for visualization.

Main Results:

  • Demonstrated the utility of dependency logos in visualizing sequence data.
  • Successfully generated dependency logos for DNA, RNA, and protein sequences.
  • Made complex dependency structures visually accessible.

Conclusions:

  • DepLogo provides a novel and effective way to visualize statistical dependencies in biological sequences.
  • The package enhances the analysis of sequence data by making hidden patterns perceptible.
  • Facilitates deeper insights into the functional roles of sequence elements.