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.

Automated nucleic acid and protein sequence annotation is accomplished using a Java-based genome annotation pipeline (unpublished), which reads an XML script containing the names and parameters of the analytical applications. The bacterial pipeline executes the gene prediction programs Glimmer (20) and GeneMark (21, 22) followed by start site correction programs RBSfinder (23) and TICO (24) . BLASTX (25) searches the non-redundant protein database, complementing the ab initio gene prediction methods. RNA genes are identified by tRNAscan-SE (26) and BLASTN searching against a ribosomal RNA database (27, 28) . The annotation protocol containing the full list of applications and parameters is available online at https://patric.vbi.vt. edu/documents/ under 'standard operating procedures'.