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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #363145

Research Project: New Genetic Resources for Breeding Better Wheat and Bioenergy Crops

Location: Crop Improvement and Genetics Research

Title: OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species

Author
item Xu, L. - Southwest University
item Dong, Z. - University Of California
item Fang, L. - Southwest University
item Luo, Y. - Southwest University
item Wei, Z. - Southwest University
item Guo, H. - Southwest University
item Zhang, G. - Southwest University
item Gu, Yong
item Coleman-derr, Devin
item Xia, Q. - Southwest University
item Wang, Y. - Southwest University

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/25/2019
Publication Date: 5/4/2019
Citation: Xu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y.Q., Coleman-Derr, D.A., Xia, Q., Wang, Y. 2019. OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 47(W1):W52-W58. https://doi.org/10.1093/nar/gkz333.
DOI: https://doi.org/10.1093/nar/gkz333

Interpretive Summary: With the rapid increase of genome sequencing data from many species across different taxa, it becomes more informant to develop useful bioinformatics tool and web applications that are suitable for data analyses on a genome wide scale. OrthoVenn was developed to provide a web server platform for comparing and analyzing orthologous genes in different species that evolved from a common ancestral gene during speciation. OrthoVenn2 is an update of OrthoVenn by providing several new features, including comparative analysis of orthologous genes from multiple species (up to twelve). It also offers improvements to data visualization and interpretation. In addition, a stand-alone version is also available to perform large dataset comparison and visualize results locally. OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net. OrthoVenn2 provides a powerful tool for identifying, analyzing and assigning biological meaning to orthologous genes and facilitates a better understanding of gene and genome evolution across diverse taxa.

Technical Abstract: OrthoVenn is a powerful web platform for comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to twelve species. We also provided a stand-alone version which can process multiple species without limitation. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species including vertebrates, metazoan, protists, fungi, plants and bacteria have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and visualize results locally. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.