Genome U-Plot

A whole genome visualization

Athanasios Gaitatzes, Sarah H. Johnson, James Smadbeck, George Vasmatzis

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Motivation The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. Results A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. Availability and implementation An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot.

Original languageEnglish (US)
Pages (from-to)1629-1634
Number of pages6
JournalBioinformatics
Volume34
Issue number10
DOIs
StatePublished - May 15 2018

Fingerprint

Genome
Visualization
Genes
Spatial Resolution
Layout
Esthetics
Sequencing
High Resolution
Metric
Aptitude
Quadruple
Chromosomes
Graph in graph theory
Documentation
Amplification
Schema
Deletion
Chromosome
Genomics
Motivation

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Genome U-Plot : A whole genome visualization. / Gaitatzes, Athanasios; Johnson, Sarah H.; Smadbeck, James; Vasmatzis, George.

In: Bioinformatics, Vol. 34, No. 10, 15.05.2018, p. 1629-1634.

Research output: Contribution to journalArticle

Gaitatzes, Athanasios ; Johnson, Sarah H. ; Smadbeck, James ; Vasmatzis, George. / Genome U-Plot : A whole genome visualization. In: Bioinformatics. 2018 ; Vol. 34, No. 10. pp. 1629-1634.
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