VIGOR, an annotation program for small viral genomes

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

VIGOR has been adjusted as well to optimally predict the protein coding genes in SARS coronavirus genomes. We downloaded from GenBank 102 annotated SARS coronavirus genomes, containing a total of 1322 annotated genes. VIGOR, GeneMarkS, and ZCURVE_V were run for these SARS coronavirus genomes to identify protein coding genes. VIGOR detected 1447 ORFs, 1321 of which completely agreed with the annotations in GenBank (Table 2) . Only one GenBank annotated gene was missing on the VIGOR prediction list. VIGOR also found 126 ORFs in these SARS coronavirus genomes which were not annotated in GenBank. By searching the NCBI NR database, the similarity search showed that these 126 newly detected genes encode proteins highly similar (E value < 1e-10) to proteins in SARS coronavirus or other viruses. ZCURVE_V predicted 1204 genes, 958 of which were identical to the annotations in GenBank. One hundred seven ZCURVE_V predictions have different start codons compared to the annotations in GenBank ( Table 2 ). This program also detected 76 new ORFs which did not exist in GenBank; as with VIGOR, the encoded proteins are highly similar to other viral proteins in Gen-Bank (data not shown). Sixty-three predictions may be incorrect since they could not be corroborated by similarity searches. These were either small peptides (shorter than 50 aa) or were located within the first long open reading frame.