J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
Nucleic Acids Res. 2012 Dec;40(22):e172. doi: 10.1093/nar/gks757. Epub 2012 Aug 16.
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.
泛基因组直系同源聚类工具（PanOCT）是一种用于分析密切相关的原核生物物种或菌株的泛基因组的工具。PanOCT 使用保守的基因邻域信息将最近分化的旁系同源物分离到同源聚类中，而同源聚类方法无法做到这一点。使用同一细菌物种的四个公开菌株集，比较了 PanOCT 和三种常用基于图的直系同源物发现程序的结果。所有四种方法在约 70%的聚类和约 86%的蛋白质上达成一致。对于不一致的聚类，我们检查了其正确性的证据，最终得到了 85 个高可信度的手动整理聚类，用于比较所有四种方法。
