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The Genome Context Viewer is a web application for identifying, aligning, and visualizing genomic regions based on their micro and macrosyntenic structures. By using functional elements such as gene annotations as the unit of search and comparison, the Genome Context Viewer can compute and display relationships between regions across many assemblies from federated data sources in real-time, enabling users to rapidly explore multiple annotated genomes and identify divergence and structural events that can help provide insight into evolutionary mechanisms associated with functional consequences. In this work, we introduce version 2 of the Genome Context Viewer and highlight new features that enhance usability, performance, and ease of deployment., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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.

Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the 'Legume Federation' project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs., (Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.)