{ * Smarty * } VIGOR: Instructions


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.

  1. Click on the download link.
  2. When the "File Download" dialog box displays, click "Save".
  3. Select a folder to download the file into and click "Save".
  4. In the "Download Complete" dialog box, click on "Open Folder".
  5. Find the downloaded file (results.gz) for Microsoft Internet Explorer browser/(results.tgz) for Firefox browser, and double-click on it.
  6. In the "User Account Control" dialog box, click "Yes" to allow WinZip to proceed.
  7. 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.
  8. The next "WinZip" dialog box asks whether to decompress it to a temporary folder and open it, click "Yes".
  9. 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".
  10. Select the folder where you like to save your result files in the pop-up window, click on "Extract".
  11. The four files (cds.pred, orf.pred, clustalw.aln and vigor2tbl.tbl) should be available in the folder you selected.
  12. The files can be opened in Microsoft Word.

Examples of VIGOR output sequence headers:

Influenza viruses.

>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.

SARS coronaviruses.

>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

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