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Welcome to the PanOCT wiki!

PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to accurately place proteins into orthologous clusters.

Literature citation:

PanOCT: Automated Clustering of Orthologs using Conserved Gene Neighborhood for Pan-Genomic Analysis of Bacterial Strains and Closely Related Species. Derrick E. Fouts, Lauren Brinkac, Erin Beck, Jason Inman, and Granger Sutton. Nucleic Acids Res 2012 Aug 16. Epub ahead of print.
http://www.ncbi.nlm.nih.gov/pubmed/22904089

** Presentation on PanOCT: **

See Dr. Sutton's talk on PanOCT at The 13th Genomic Standards Consortium Meeting (GSC 13). Hosted by BGI and held at Kingkey Palace Hotel, Shenzhen, China, March 4-7, 2012: http://www.scivee.tv/node/46402

Memory usage guide (based on 4 Mbp bacterial genomes)

Memory	# genomes
1 GB RAM	1-5
2 GB RAM	1-8
4 GB RAM	1-12
8 GB RAM	1-18
14 GB RAM	1-25

*Note: This is only meant as a guide. Performance may very. Results not guaranteed.

Screenshots

PanOCT Memory Usage Plot

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[Derrick Fouts]

Adding supplemental files from the manuscript since the links at NAR appear to not work for everyone.