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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 #314309

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

Author
item Wang, Yi - University Of California
item Coleman-derr, Devin
item Chen, Guoping - Chongqing University
item Gu, Yong

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2015
Publication Date: 5/11/2015
Citation: Wang, Y., Coleman-Derr, D.A., Chen, G., Gu, Y.Q. 2015. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 43(W1):W78-W84. doi: 10.1093/nar/gkv487.

Interpretive Summary: Our understanding of plant biology and evolution has been greatly aided by recent advances in DNA sequencing technology and the development of comparative methods for genome analysis. With the rapid increase in genome sequencing data, it becomes more important to develop useful bioinformatics tools and applications that are suitable for data analysis on a genome wide scale. Here, OrthoVenn is 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. A number of useful features are employed in this web server application, including an interactive Venn Diagram tool that shows the relationships of overlap and non-overlap orthologous genes among multiple species selected, a comprehensive annotation for all the proteins in the database, and a search function for specific genes of interest for further sequence alignment and phylogenetic analysis. In addition, users can add new sequence data from species not already covered in the database. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn. We think OrthoVenn provides a powerful platform 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: Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome-wide comparisons and annotation of orthologous clusters. OrthoVenn provides comprehensive coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, statistical analyses, and function summaries of the non-overlapping and overlapping portions of the clusters are displayed in the OrthoVenn result. OrthoVenn also includes a comprehensive annotation of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies ortholog clusters of single copy genes and allows searches of specific gene ortholog clusters through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn. Database URL: http://probes.pw.usda.gov/AIM