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EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae
Liliana Florea1, Michael McClelland, Cathy Riemer
1Informatics Research, Celera/Applied Biosystems, 45 W. Gude Drive, Rockville, MD 20850, USA. liliana.florea@celera.com
Nucleic Acids Research
|June 26, 2003
Summary
EnteriX provides three web tools to visualize enterobacterial genome alignments, aiding in comparative genomics for pathogenicity and phylogenetic studies. These tools help analyze genomic rearrangements and identify conserved regulatory sites across related species.
Area of Science:
- Comparative genomics
- Bioinformatics
- Genomic visualization
Background:
- Comparative analysis of related bacterial genomes is crucial for understanding evolution, pathogenicity, and phylogenetic relationships.
- Visualizing large-scale genomic alignments and identifying conserved regions presents significant computational and analytical challenges.
Purpose of the Study:
- To introduce EnteriX, a suite of three integrated web-based visualization tools designed for graphical representation of alignment data from enterobacterial species.
- To facilitate the examination of genomic commonalities and differences, identification of conserved regulatory sites, and exploration of pathogenicity and phylogenetic relationships.
Main Methods:
- Development of three distinct visualization tools: Enteric (PIP-based pairwise alignments), Menteric (nucleotide-level multiple alignments with annotations), and Maj (Java-based with zoom capabilities).
- Anchoring alignments on a reference genome and incorporating both fixed and user-supplied sequences from related enterobacterial species.
- Utilizing schematic representations like Percent Identity Plots (PIPs) to encode large-scale genomic rearrangements and functional landmarks.
Main Results:
- EnteriX offers diverse visualization formats, including stacked pairwise alignments and detailed nucleotide-level multiple alignments.
- The suite supports comparisons across >15 enterobacterial genomes, with options to use four different anchor genomes and include user sequences.
- Visualizations highlight genomic rearrangements, functional landmarks, genes, regulatory sites, and conserved regions.
Conclusions:
- The EnteriX suite provides a powerful and versatile platform for exploring and analyzing comparative genomic data in enterobacteria.
- These visualization tools can significantly aid researchers in diverse applications, including pathogenicity studies, phylogenetic analysis, and the discovery of functional genomic elements.