- About VIGOR
- Run VIGOR
- Instructions & Test Samples
- Influenza virus
- Measles & mumps virus
- Parainfluenza & Sendai virus
- Respiratory syncytial virus (RSV)
- Rubella virus
- Venezuelan equine encephalitis virus & alphavirus
- West Nile virus & Dengue virus
- Yellowfever & Japanese encephalitis virus
VIGOR - VIRAL GENOME ORF READER
VIGOR (Viral Genome ORF Reader) is a web application tool to predict protein sequences encoded in small viral genomes, i.e., alphavirus, corovavirus, influenza virus, Japenese encephalitis virus (JEV), measles virus, metapneumovirus (MPV), mumps virus, norovirus, parainfluenza virus (PIV), respiratory syncytial virus (RSV), rhinovirus, rotavirus, Rubella virus, SARS coronavirus, Sendai virus, Venezuelan equine encephalitis virus (VEEV) and yellow fever virus (YFV). VIGOR determines the protein coding sequences by sequence similarity searching against curated viral protein databases. Four output files will be generated by VIGOR prediction, a gene prediction file (including predicted protein sequences and annotations), a predicted FASTA format cDNA file, a file of the alignment between the predicted protein and the best homolog in the custom database, and a TBL file that can be used to generate GenBank submission by Sequin and tbl2asn.
To run the prediction on your sequence(s), either paste the nucleotide FASTA record(s) into the textbox or upload your FASTA file by clicking on the "Browse" button. A description of the FASTA format is provided at NCBI.
Before you submit your sequence(s), please select the virus type which you are analyzing, and enter your email address as well, therefore you can be notified once the prediction result is available.
When you click on the "Submit" button, your sequence(s) will be queued and an email will be sent to you to confirm receipt. Once the prediction has been executed, you will receive another email notification indicating how you may view the results.
Click here to get Test Sequence Samples.
Instructions for downloading result tarball in Windows 7.
- Click on the download link.
- When the "File Download" dialog box displays, click "Save".
- Select a folder to download the file into and click "Save".
- In the "Download Complete" dialog box, click on "Open Folder".
- Find the downloaded file (results.gz) for Microsoft Internet Explorer browser/(results.tgz) for Firefox browser, and double-click on it.
- In the "User Account Control" dialog box, click "Yes" to allow WinZip to proceed.
- In the "WinZip" filename dialog box type "results.tar" (this instructs WinZip to handle the content as a tar) and then click "OK"; for Firefox browser, the default file name is "results.tar", skip this step.
- The next "WinZip" dialog box asks whether to decompress it to a temporary folder and open it, click "Yes".
- In the "WinZip-results.tar" dialog box, four files (cds.pred, orf.pred, clustalw.aln and vigor2tbl.tbl) are listed in the file name window, click on "Extract".
- Select the folder where you like to save your result files in the pop-up window, click on "Extract".
- The four files (cds.pred, orf.pred, clustalw.aln and vigor2tbl.tbl) should be available in the folder you selected.
- The files can be opened in Microsoft Word.
Examples of VIGOR output sequence headers:
>FJ966982.1.1 HA H1 566 Aa 1 1701 hemagglutinin [influenza A virus] >FJ966981.1.1 NA N1 469 Aa 1 1410 neuraminidase [Influenza A virus] pep_ID Gen_Symb Genotype pep_len CDS_coord product_name viral_group.
>AB049167.2 NS2 121 Aa 1 30, 503 838 nonstructural protein 2 [Influenza A virus] Pep_ID Gen_Symb pep_len CDS_coord(splicing) product_name viral_group.
>445.2 7073 Aa 246..13379, 13379..21466 polyprotein orf1ab pep_ID pep_len CDS_coord(ribosomal slippage) product_name
>445.3 1255 Aa 21473 25240 spike glycoprotein precursor
pep_ID pep_len CDS_coord product_name
>489.1.4 8465 9964 mat_peptide nsp4 mat_pep_ID coding_region_coord mat_pep_name