VIGOR, an annotation program for small viral genomes

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

VIGOR usage in high-throughput viral genome closure and annotation VIGOR has been used extensively to validate the genomes in the finishing process for the high-throughput virus sequencing projects at JCVI [21] [22] [23] [24] [25] 30] . In this role, VIGOR is used to detect sequence changes which generate a premature stop codon or a frameshift. The potential sequence error and the flanking sequences as well as the BLASTX alignment results are presented in the prediction output. This data allows researchers working on finishing tasks to investigate whether the sequence changes are due to laboratory error or are biologically relevant SNPs or IN/DELs. We noticed that if a mutation or a sequence error generates a pre-mature stop codon or causes frame-shift, and the translated product still meets all criteria stated above, VIGOR will predict this gene as a functional gene. In this type of cases, VIGOR prediction may not be able to identify the potential sequence errors. However, VIGOR provides the alignment data between the predicted peptide and reference sequence in the output alignment file, users can use the alignment data to evaluate the prediction and identify the potential sequence errors. If a genomic sequence covers only a fraction of a gene coding region, VIGOR will identify this genomic sequence as partial sequence. Genome finishing team is able to pursue finishing the genome basing the missing regions identified by VIGOR.