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- Title
PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species.
- Authors
Fouts, Derrick E; Brinkac, Lauren; Beck, Erin; Inman, Jason; Sutton, Granger
- Abstract
Pan-genome ortholog clustering tool (PanOCT) is a tool for pan-genomic analysis of closely related prokaryotic species or strains. PanOCT uses conserved gene neighborhood information to separate recently diverged paralogs into orthologous clusters where homology-only clustering methods cannot. The results from PanOCT and three commonly used graph-based ortholog-finding programs were compared using a set of four publicly available strains of the same bacterial species. All four methods agreed on ∼70% of the clusters and ∼86% of the proteins. The clusters that did not agree were inspected for evidence of correctness resulting in 85 high-confidence manually curated clusters that were used to compare all four methods.
- Publication
Nucleic acids research, 2012, Vol 40, Issue 22, pe172
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gks757