PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species.
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.
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA. dfouts@jcvi.org
Derrick E
DE
Fouts
Lauren
L
Brinkac
Erin
E
Beck
Jason
J
Inman
Granger
G
Sutton
D001419:Bacteria / Q000145:classification; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics*; D016000:Cluster Analysis; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D012984:Software
D001426:Bacterial Proteins