At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid.
AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.
Revised: May 1, 2014 |
Published: October 15, 2013
Citation
Curtis D.S., A.R. Phillips, S.J. Callister, S. Conlan, and L.A. McCue. 2013.SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes.Bioinformatics 29, no. 20:2641-2642.PNNL-SA-94621.doi:10.1093/bioinformatics/btt454