title: SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  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.
authors: Computational & Statistical Analytics Division, Pacific Northwest National Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA, Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA and Computational Sciences & Mathematics Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors: Darren S
authors: DS
authors: Curtis
authors: Aaron R
authors: AR
authors: Phillips
authors: Stephen J
authors: SJ
authors: Callister
authors: Sean
authors: S
authors: Conlan
authors: Lee Ann
authors: LA
authors: McCue
mesh_terms: D016678:Genome; D023281:Genomics / Q000379:methods*; D020407:Internet; D011381:Programming Languages; D011506:Proteins / Q000235:genetics; D012985:Software Design
chemical_list: D011506:Proteins
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