Dataset Information

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV).

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 NCBI using assembly alignment algorithms developed by us and others. Researchers can examine the alignments between the two assemblies using two alternate views: a chromosome ideogram-based view or a 2D genome dotplot. Whole genome alignment views expose 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 in the ideogram view where available. CGV currently provides approximately 700 alignments from over 300 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.

SUBMITTER: Rangwala SH

PROVIDER: S-EPMC10705539 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV).

Rangwala Sanjida H SH Rudnev Dmitry V DV Ananiev Victor V VV Asztalos Andrea A Benica Barrett B Borodin Evgeny A EA Bouk Nathan N Evgeniev Vladislav I VI Kodali Vamsi K VK Lotov Vadim V Mozes Eyal E Oh Dong-Ha DH Omelchenko Marina V MV Savkina Sofya S Sukharnikov Ekaterina E Virothaisakun Joël J Murphy Terence D TD Pruitt Kim D KD Schneider Valerie A VA

bioRxiv : the preprint server for biology 20231129

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 NCBI using assembly alignment algorithms developed by us and others. Researchers can examine the alignments between the two assemblies using two alternate views: a chromosome ideogram-based view or a 2D genome dotplot. Whole genome alignment views expo ...[more]

PMID: 38077029

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Project description:BackgroundIn recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences.ResultsIn this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments.ConclusionsMultiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

Dataset Information

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV).

Publications

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV).

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