VIGOR, an annotation program for small viral genomes

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

GeneMarkS detected only 941 genes and 680 of them were precise predictions. One hundred nineteen predictions hit the correct regions with the correct frame but the start codons were incorrect ( Table 2) . GeneMarkS also picked 21 new ORFs which are similar to other viral proteins. One hundred twenty-one GeneMarkS predictions may be incorrect since no homologous proteins could be found in GenBank. Two hundred fiftyseven and 523 GenBank annotations were missing on the ZCURVE_V and GeneMarkS prediction list. These missing genes were examined closely, and most of them are overlapping genes, such as, non-structural protein 3b, 9b, envelope protein, or the gene encoding a nonstructural protein which is completely embedded within the coding region of nucleocapsid protein.