VIGOR, an annotation program for small viral genomes

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

A user needs to select the virus type through a pulldown virus name menu prior to submitting the sequence data. The user will be informed of the link to download the prediction result by email following the VIGOR run. The output includes three files. The main output file is the gene prediction file which includes the predicted peptide sequence length, coordinates of the coding regions, splice sites if applicable, protein function and genotype if available, and the predicted amino acid sequences. The other two output files are the cDNA sequence file and a file of the alignment between the predicted protein and the best match in the custom database so that the user can evaluate the prediction. If mutations which generate internal stop codons or frameshifts are detected, the mutated sequences plus the flanking sequences will be presented in the output. The alignment data from the BLASTX search is also included in the gene prediction file.