Abstract
BackgroundThe volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets.ResultsIn this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process.ConclusionsBactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.
Highlights
Bacterial genomes–the complete set of genes or genetic material present in bacteria–play an important role in several fields, from the study of micro-biomes to drug development
Bacterial genome sequencing, which determines the complete nucleotide sequence in a bacterial strain’s DNA, is increasing at rates that exceed Moore’s Law [1], since these genomes are relatively small and inexpensive to sequence. These emerging large collections of complete genome sequence data from bacterial strains are changing the landscape of comparative bacterial genomics
Comparative genomics is broadly concerned with comparing genomic features across several genomes, to address questions pertaining to evolution and explain variations in different organisms
Summary
We present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process
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