title: OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.
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 visualization of orthologous clusters. OrthoVenn provides 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, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn.
authors.affiliation: USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA Department of Plant Sciences, University of California, Davis, CA 95616, USA Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China Yi.Wang@ars.usda.gov.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
authors.forename: Devin
authors.initials: D
authors.lastname: Coleman-Derr
authors.affiliation: Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China.
authors.forename: Guoping
authors.initials: G
authors.lastname: Chen
authors.affiliation: USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA Yi.Wang@ars.usda.gov.
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010802:Phylogeny; D020539:Sequence Analysis, Protein; D012984:Software