PATRIC: The VBI PathoSystems Resource Integration Center

Snyder, E. E.; Kampanya, N.; Lu, J.; Nordberg, E. K.; Karur, H. R.; Shukla, M.; Soneja, J.; Tian, Y.; Xue, T.; Yoo, H.; Zhang, F.; Dharmanolla, C.; Dongre, N. V.; Gillespie, J. J.; Hamelius, J.; Hance, M.; Huntington, K. I.; Jukneliene, D.; Koziski, J.; Mackasmiel, L.; Mane, S. P.; Nguyen, V.; Purkayastha, A.; Shallom, J.; Yu, G.; Guo, Y.; Gabbard, J.; Hix, D.; Azad, A. F.; Baker, S. C.; Boyle, S. M.; Khudyakov, Y.; Meng, X. J.; Rupprecht, C.; Vinje, J.; Crasta, O. R.; Czar, M. J.; Dickerman, A.; Eckart, J. D.; Kenyon, R.; Will, R.; Setubal, J. C.; Sobral, B. W. S.

Once protein sequences are inferred from each genome in an organism category, putative ortholog groups are generated using BLASTP for all pairwise genome combinations and applying the conventional bidirectional-best-hit (BBH) criterion (33) . While putative ortholog groups within the bacterial categories are generally well defined, many viral proteins cannot be readily clustered using the stringent BBH criterion. This is an active area of curation. Using the ortholog groups as a starting point, a reference protein list is created for each bacterial category consisting of the proteins of the reference genome (each representing one ortholog group) plus a representative protein from each ortholog group identified in the associated genomes. A gene occurring in only a single genome constitutes a 'group' of one and would be included in the reference list. The reference protein lists will be manually curated and include, whenever possible, detailed functional descriptions, gene symbols, GO terms and EC numbers. Thus, every protein in the database will either be manually curated or be linked to an ortholog group member that has been manually curated.