SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes

Journal Article · Tue Oct 15 00:00:00 EDT 2013 · Bioinformatics, 29(20):2641-2642

DOI:https://doi.org/10.1093/bioinformatics/btt454· OSTI ID:1130673

Curtis, Darren S.; Phillips, Aaron R.; Callister, Stephen J.; Conlan, Sean; McCue, Lee Ann

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.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1130673
• Report Number(s): PNNL-SA-94621; KP1601040; KP1601010
• Journal Information: Bioinformatics, 29(20):2641-2642, Journal Name: Bioinformatics, 29(20):2641-2642
• Country of Publication: United States
• Language: English

Related Subjects

ortholog
comparative genomics