Asfarviruses and the VBRC
The VBRC provides comprehensive web-based genomics resources to the scientific community through:
- Providing up-to-date genomic and proteomic data from the virus families.
- see Organisms menu for a list of virus families supported
- Providing easy-to-use software tools to perform a variety of bioinformatics analyses.
- see Tools menu for a list of software tools
- we also build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists.
- Offering researchers help on specific bioinformatics problems.
You can find the VBRC’s mandate here and more information on the home page.
Multigene families in African Swine Fever Virus (New !!!!)
ASFV encodes 5 multigene families (MGF), each a set of paralogs. All of the paralogs of a particular set are not always in tandem, and may be at opposite ends of the linear genome and transcribed in different orientations.
Over the years, several naming schemes have been used, which complicates the comparison of the viruses. Furthermore, the loss and fragmentation of individual genes and fusion of others have made their notation even more complicated.
We have created a set of figures to illustrate what we think is a good representation of the organization of each MGF-in the 16 genomes currently available (March 2017).
Below, are links to information about each MGF, providing a hi-res figure and a figure legend.
This work was funded by the Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD) and the National Pork Board (USA).
We need the ASFV Research Community to view and validate our results. Is there a better way to display this information?
Analysis tools at the VBRC
We provide highly interactive software tools that enable users to view and analyze viral genomes. These tools can be accessed directly from the “Asfarviridae Tools” drop-down menu on the top left of this page. These tools include:
- Viral Orthologous Clusters (VOCs) allows users to easily search the Asfarviridae database for protein sequences or genes of a known function or of a specific genome and then apply different analysis techniques to the search result. VOCs provides quick and easy access to tools like BLAST, multiple alignment, dotplots, and genome statistics.
- Viral Genome Organizer (VGO) allows users to browse genomes, viewing genes, ORFs, start/stop codons, nucleic acid composition, and orthologs when working with multiple genomes.
To start work: Check the Quick Start Tutorials (well worth 5 minutes) or just dive in by selecting a tool from the menu. Our usual starting place is the VOCs, which allows you to select data for use with the analysis tools.
The VBRC provides an Asfarvirus Information Book that includes:
- Up-to-date website links to collections of published research reviews through NCBI.
- Links to other asfarvirus internet resources for general and background information.
Follow @ASFV_papers on Twitter to see what is being published about ASFV.
Genomes excluded from VOCs
- MN194591: ASFV Kyiv/2016/131
(Long read assembly not corrected by short reads; as a result, crucial genes such as DNA polymerase has fragmented ORFs)
- KP055815: ASFV BA71 (partial genome)
- MH910496: ASFV Georgia 2008/2 (partial genome)
- MN394630: ASFV SPEC_57 (Suspicious assembly and partial annotation; found long novel ORFs overlapping known ORFs)
- MN318203: ASFV LIV_5_40 (Suspicious assembly and partial annotation; found long novel ORFs overlapping known ORFs)
- MN336500: ASFV RSA_2_2008 (Suspicious assembly and partial annotation; found long novel ORFs overlapping known ORFs)
Problematic Genomes included in VOCs