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Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV)
Sanjida H Rangwala1, Dmitry V Rudnev1, Victor V Ananiev1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Biorxiv : the Preprint Server for Biology
|December 11, 2023
Summary
The Comparative Genome Viewer (CGV) is a new tool for analyzing whole genome alignments. It helps researchers visualize and detect structural variations across species.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Comparative genomics relies on accurate visualization of whole genome alignments to understand evolutionary relationships and identify structural variations.
- Existing tools may not offer comprehensive visualization of large-scale and small-scale genomic differences across diverse species.
Approach:
- Developed the Comparative Genome Viewer (CGV), a novel visualization tool for analyzing pairwise genome assembly alignments.
- CGV supports both same-species and cross-species alignments, utilizing established and novel alignment algorithms.
- Provides two distinct visualization modes: a chromosome ideogram-based view and a 2D genome dotplot for detailed analysis.
Key Points:
- CGV facilitates the identification of large-scale structural differences, including inversions and translocations, across entire chromosomes.
- Enables detailed examination of smaller genomic variations such as deletions and rearrangements within specific regions or genes.
- Integrates RefSeq or user-provided gene annotations within the ideogram view for enhanced context.
- Currently offers access to approximately 700 alignments from over 300 diverse species (animal, plant, fungal).
Conclusions:
- The Comparative Genome Viewer (CGV) offers a powerful new platform for comparative genome visualization and analysis.
- Ongoing development aims to further enhance CGV's capabilities to meet the evolving needs of the research community in comparative genomics.
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