Description:
What it is: an ortholog and paralog prediction algorithm that provides interactive visualizations of the ortholog/paralog clusters
What it does: SPOCS is designed to identify orthologous and paralogous proteins from a group of closely related prokaryotes, and to provide a visualization of the homologous relationships between proteins. The software will merge reciprocal best BLAST hits between pairs of species, generating undirected graphs, i.e., clusters of orthologs and paralogs, then identify the cliques from these undirected graphs. The visualization of the orthologous clusters and cliques can be enhanced by overlaying experimental data from gene or protein expression experiments.
Species Paralogy and Orthology Clique Solver (SPOCS) is a graph-based ortholog/paralog prediction tool that will predict orthologs and paralogs given a set of prokaryotic proteomes (the set of proteins encoded by a genome). The software will take a set of protein fasta files (one per species genome), and an optional additional fasta to serve as an outgroup (a species that should be more distantly related to the species of interest than any of the species of interest are to each other). BLAST is required to generate the reciprocal best hit results for every pair of species. SPOCS then merges these results identifying orthologs using the graph-based concept of cliques. Detailed installation instructions are included in the download.
Availability
SPOCS can be run using our web application here. The software is also freely available for installation on Linux systems, under an open source license. The license can be viewed here, and is also included in the User Guide and the software README file. Downloading the software from the “Mac OSX/Linux Download” button below constitutes your acceptance of these license terms.
Mac OSX/Linux Download
User Guide Download
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