VIGOR, an annotation program for small viral genomes

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

The rhinovirus genome encodes one polyprotein precursor which is cleaved into eleven functional mature peptides [20] . Thirty-six annotated rhinovirus genomes were downloaded from GenBank and tested with VIGOR, GeneMarkS and ZCURVE_V. VIGOR correctly predicted the polypeptide start codon and stop codon, as well as the mature peptides for each genome (see Table 2 ). GeneMarkS identified all 36 polyproteins, but predicted the wrong start codons for four genomes. An additional nine small ORFs were incorrectly predicted in the 5'-UTR. ZCURVE_V predicted 77 genes in total, including the 36 true ORFs and 41 mis-predicted small peptides. The start codons of 6 real open reading frames were not correctly predicted. VIGOR was also used to predict the polyproteins and mature peptides for 66 ATCC rhinovirus samples and field samples sequenced at JCVI with 100% specificity and sensitivity [21] . Neither GeneMarkS nor ZCUR-VE_V was designed to predict mature peptide sequences for viral genomes.