VIROME analysis application

Viral Informatics Resource for Metagenome Exploration - VIROME

VIROME is a web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts.

The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. For information on the VIROME bioinformatic pipeline visit the Methods page. All ORFs receive only one classification based on the following priority:

VIROME ORF and sequence categories
  • 1. Ribosomal RNA containing sequences
    Reads with significant homology to 5S, 16/18S, or 23/25S rRNA.
  • 2. Transfer RNA containing sequences
    Reads with significant homology to a tRNA
  • 3. Possible functional protein
    ORFs with significant homology to a protein having a functional classification in the UniRef 100 plus database.
  • 4. Unassigned protein
    ORFs with significant homology to a protein with unassigned function in the UniRef 100 plus database.
  • 5. Top-hit viral environmental protein
    ORFs with significant homology to only environmental sequence, top hit was of viral in origin within the MetaGenomes on-line database
  • 6. Viral only environmental protein
    ORFs with significant homology to only environmental sequence, all hits were of viral in origin within the MetaGenomes on-line database.
  • 7. Top-hit microbial environmental protein
    ORFs with significant homology to only environmental sequence, top hit was of microbial in origin within the MetaGenomes on-line database.
  • 8. Microbial only environmental protein
    ORFs with significant homology to only environmental sequence, all hits were of microbial in origin within the MetaGenomes on-line database.
  • 9. True ORFan
    BLAST analysis against over 50 million proteins yielded no significant homology in either the UniRef 100 plus or MetaGenomes on-line databases.


VIROME Tutorial videos
  • VIROME Overview tutorial
  • This video tutorial covers the basic features of the Viral Informatics Resource for Metagenome Exploration. Use the You Tube video menu bar to view in full 1080p.
  • Downloading whole libraries of VIROME data
  • The video tutorial shows how to download entire libraries of viral metagenome sequence data from the Viral Informatics Resource for Metagenome Exploration. Use the You Tube video menu bar to view in full 1080p.
  • Discovering new genetic polymorphism with VIROME
  • This video tutorial covers the use of VIROME to discover novel genetic polymorphism within viral metagenomic libraries. Use the You Tube video menu bar to view in full 1080p.
  • Comparative metagenomic analysis using VIROME
  • This video tutorial covers the use of VIROME data for comparative analysis of viral communities using the Quantitative Insights in Microbial Ecology package (QIIME). Use the You Tube video menu bar to view in full 1080p.


VIROME is the collective creative and scientific output of principally: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack. If you use VIROME in the preparation of data for publication please give the URL (http://virome.dbi.udel.edu) and cite:

Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967]

VIROME development supported through research grants from the Gordon and Betty Moore Foundation, the National Science Foundation, the US. Department of Agriculture, and the Delaware EPSCoR program