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.

Results of the genome analysis pipeline are merged with original GenBank or RefSeq features for automated interpretation. A decision tree is used to classify genes into categories based on the level of agreement between the various prediction methods. Genes that are unambiguously predicted by multiple methods are automatically 'finalized', creating new 'gene', 'CDS' and/or '[t/r]RNA' features. The remaining genes are marked for manual curation. For viral genomes, an abbreviated pipeline is executed that emphasizes sequence alignment for gene identification and employs GeneMarkHMM optimized for mammalian (host) genomes.