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. 2018 May 1;34(9):1562-1564.
doi: 10.1093/bioinformatics/btx757.

Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny

Alan Cleary  1   2 , Andrew Farmer  2
Affiliations

Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny

Alan Cleary et al. Bioinformatics. .

Abstract

Summary: The Genome Context Viewer is a visual data-mining tool that allows users to search across multiple providers of genome data for regions with similarly annotated content that may be aligned and visualized at the level of their shared functional elements. By handling ordered sequences of gene family memberships as a unit of search and comparison, the user interface enables quick and intuitive assessment of the degree of gene content divergence and the presence of various types of structural events within syntenic contexts. Insights into functionally significant differences seen at this level of abstraction can then serve to direct the user to more detailed explorations of the underlying data in other interconnected, provider-specific tools.

Availability and implementation: GCV is provided under the GNU General Public License version 3 (GPL-3.0). Source code is available at https://github.com/legumeinfo/lis_context_viewer.

Contact: adf@ncgr.org.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
A GCV search view exhibiting copy number presence/absence/variation and structural rearrangements. (lower left) Micro-synteny relationships generated from search results aligned with the Repeat algorithm to capture inversion. (upper left) Precomputed macro-synteny blocks indicating the chromosome-scale context of the micro-synteny tracks below. (lower right) A local dot plot of the query track and a selected result track, giving a complementary view of microsynteny features. (upper right) Gene family legend with focus family highlighted (Color version of this figure is available at Bioinformatics online.)
See this image and copyright information in PMC

References

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    1. Dash S. et al. (2016) Legume information system (legumeinfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Research, 44, D1181–D1188. - PMC - PubMed
    1. Durbin R. et al. (1998) Biological Sequence Analysis: probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.

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