The basis for the calculation of the subVOGs are the Virus Orthologous Groups (VOGs), provided by the university of Vienna; subVOGs are structurally homogenous groups of viral mRNAs within VOGs. A VOG is split into subVOGs by first producing a neighbor joining distance tree of all mRNA sequences within that VOG. All sequences of the inner nodes of the tree, representing potential subVOGs, are aligned and scanned for conserved RNA structures. Regions with potentially conserved structures are realigned with the structure guided alignment method mLocARNA, and functionally annotated using RNAz. Tree nodes containing the most sequences that yield conserved structures are taken as final subVOGs.
-search for structurally conserved regions in viral mRNAs
-search for structurally related sequences of viral mRNAs
-limit sequence space for experimental structure determination of viral mRNAs
The subVOGs were built in a joint effort of the Department of Bioinformatics of the Technical University of Munich, the Department of Computational Systems Biology (CUBE) and the Theoretical Biochemistry Group (TBI) of the University of Vienna.