Viral Bioinformatics Resource Center - Central Tools Provided By VBRC

Central Tools Provided By VBRC

VBRC provides researchers with a wide variety of database-linked tools. Of these, the central four programs are VOCs, VGO, BBB, and JDotter.

1. VOCs (Viral Orthologous Clusters)
   VOCs is the main database access interface. Users can search the available data by a number of criteria related to genome, gene, or ortholog group characteristics. Search results are displayed in table format; from here the user may obtain further information about a particular database entry, or launch a VOCs-linked tool (see below) for analysis of selected data. Additional analysis tools such as BLAST searches, genome maps, genome or gene alignment, phylogenetic trees, etc. are provided.
2. VGO (Viral Genome Organizer)
   VGO is a Java-based interface used for viewing and searching viral genome sequences. Together with a graphical representation of the selected VBRC (or user-supplied) genome, the program displays information relevant to a genome of interest, including its genes, ORFs and start/stop codons. Tools are provided allowing the user to perform regular expression, a fuzzy motif, and masslist searches. VGO can also be used to identify related genes across multiple sequences.
3. BBB (Base-by-Base)
   Base-By-Base is a platform-independent (Java-based), whole-genome pairwise and multiple alignment editor. The program highlights differences between consecutive pairs of sequences within an alignment, thus allowing the user to survey a large alignment at a single-residue level. Annotations from the VBRC database or user-supplied files are displayed alongside each sequence.
   Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it also generates multiple alignments using ClustalW, T-Coffee and MUSCLE. Edit functions are provided to allow users to fine-tune such alignments manually; users may also annotate genomes with comments or primer sequences.
4. JDotter
   JDotter is a Java-based user interface providing VBRC-linked access to the Linux version of Dotter. JDotter can both access pre-processed dotplots of the genome and gene (DNA or protein) sequences available in the VBRC database, and take user input for generation of new dotplots. JDotter also interfaces with the curated database or the user-supplied file to display supplementary feature data such as gene annotations.