Version 1.0.5; March 2020
VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus and Dengue virus sequences in preparation for submission to the GenBank database.
v-annotate.pl script is used to classify a sequence, by
determining which in a set of reference models it is most similar
to, and then annotate that sequence based on that most similar model.
Example usage of
v-annotate.pl can be found here.
Another VADR script,
v-build.pl, is used to create the models from
NCBI RefSeq sequences or from input multiple sequence alignments,
potentially with secondary structure annotation.
the RefSeq feature annotation in the model, and
that annotation (e.g. CDS coordinates) onto the sequences it
annotates. VADR includes 197 prebuilt models of Flaviviridae and
Caliciviridae viral RefSeq genomes, described
here. Example usage of
v-build.pl can be
v-annotate.pl identifies unexpected or divergent attributes of the
sequences it annotates (e.g. invalid or early stop codons in CDS
features) and reports them to the user in the form of alerts. A
subset of alerts are fatal and cause a sequence to fail. A
sequence passes if zero fatal alerts are reported for it. VADR is
used by GenBank staff to evaluate incoming sequence submissions of
some viruses (currently Norovirus and Dengue virus). Submitted
sequences that pass
v-annotate.pl are accepted into GenBank.
The homology search and alignment components of VADR scripts, the most computationally expensive steps, are performed by the Infernal and BLAST software packages, which are downloaded and installed with VADR installation.
You can download pre-built models to use to validate and
annotate viruses or cox1 genes as listed below. Importantly,
to use a set of models other than the default set that is
installed with VADR, you will need to use use the
-b options as described here.
Pre-built models are available for:
- Norovirus and Dengue virus RefSeqs, along with other Flaviviridae and Caliciviridae RefSeqs (this is the "default" set of models that is installed with VADR)
- Coronaviridae RefSeqs, including 2019-nCoV (NC_045512)
- metazoan Cytochrome c oxidase I (COX1)
See this page for more information
- VADR installation instructions
v-build.plexample usage and command-line options
v-annotate.plexample usage, command-line options and alert information
- VADR output file formats
- Available VADR model files
- The recommended citation for using VADR is: Alejandro A Schaffer, Eneida L Hatcher, Linda Yankie, Lara Shonkwiler, J Rodney Brister, Ilene Karsch-Mizrachi, Eric P Nawrocki; VADR: validation and annotation of virus sequence submissions to GenBank; bioRxiv 852657; doi: https://doi.org/10.1101/852657.