The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments

PLoS Biol. 2024 May 7;22(5):e3002405. doi: 10.1371/journal.pbio.3002405. eCollection 2024 May.

Abstract

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

MeSH terms

  • Algorithms
  • Animals
  • Databases, Genetic
  • Eukaryota / genetics
  • Genome* / genetics
  • Genomics / methods
  • Humans
  • Molecular Sequence Annotation / methods
  • National Library of Medicine (U.S.)
  • Sequence Alignment / methods
  • Software*
  • United States

Grants and funding

This work was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.