About VIROME

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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.

Reference VIROME

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