VIGOR, an annotation program for small viral genomes

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

To evaluate the performance of VIGOR for coronavirus gene prediction, 38 annotated complete coronavirus genomes containing annotation for 341 genes were downloaded from GenBank and run through VIGOR, GeneMarkS and ZCURVE_V. VIGOR identified 354 ORFs, while GeneMarkS and ZCURVE_V predicted 314 and 339 protein coding genes respectively (Table 2) . Of the 341 GenBank annotated genes, VIGOR correctly predicted 339 genes, missed one gene and identified one gene with wrong start codon ( Table 2) . VIGOR also predicted 14 new ORFs which were not annotated in Gen-Bank. Manual curation of these 14 newly predicted proteins showed that they are highly similar (E value < 1e-10) to annotated coronavirus or other viral proteins (data not shown); thus we classified these 14 newly identified genes in coronaviruses as correct predictions. Of the 341 annotated genes, GeneMarkS and ZCUR-VE_V did not detect 48 and 34 genes respectively. Most of the missing genes were short overlapping genes. The small structural envelope protein coding gene in 10 coronavirus genomes was not identified by either of these two programs because the coding region of this envelope protein overlaps with the coding region of an upstream gene.