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.

The organism category page also contains links to a pathogen summary, ortholog group table and a phylogenetic tree based on 16S rRNAs for bacteria or a selected protein family for viruses. For bacterial genomes, detailed pathosystem information is available, provided by the VBI PathInfo documents (14) . The ortholog group table shows the presence or absence of reference gene list proteins for each organism in the organism category and provides links to an MSA and tree viewer and the Base-By-Base MSA editor (38) for every ortholog group. Base-By-Base allows users to add sequences to the MSA, recalculate it using Clustal (39) , T-Coffee (40) or MUSCLE and generate the corresponding tree using neighbor-joining or a number of clustering algorithms.