VIGOR, an annotation program for small viral genomes

Wang, Shiliang; Sundaram, Jaideep P; Spiro, David

The influenza virus genome consists of eight RNA segments that encode one or two proteins each. Splicing is involved in the expression of the MP and M2 proteins from segment 7 (MP segment) in group A influenza viruses and NS1 and NS2 proteins from segment 8 (NS segment) in both group A and group B viruses [16] . Segment 2 (PB1 segment) encodes two proteins, PB1 and PB1-F2, in some influenza genomes. The coding sequence of PB1-F2 is completely embedded in the PB1 coding region with a different reading frame [17] . In order to test its accuracy in gene finding, 2376 full and partial influenza segment sequences including group A, group B, and group C viruses, encoding 3177 annotated proteins, were run through VIGOR. VIGOR predicted 3178 ORFs encoded by these segments. Among these predicted protein sequences, 99% (3169/3178) ORFs completely agreed with the annotations in GenBank. Three predicted ORFs were partially correct and one ORF was incorrectly predicted ( Table 1) .