The Main Windows Menu Bar
The File Menu
“Choose Database”: change the VOCs database by selecting the viral family name within which you would like to work
“Preferences”: define default preferences (ie. window size, window location on screen, program preferences, default parameters for BLAST searches etc.) for VOCs windows and applications such as BLAST, Clustalw, JDotter, Muscle, Needle, TCoffee etc.
“Quit”: exit VOCs
The Select Menu
“Clear All”: reset all search parameters to the respective default values
The View Menu
“Virus data (Annotated Genomes/Unannotated Genomes)”: view genome data (for either annotated or unannotated genomes)
“Virus upstream sequences”: view sequences upstream of genes
“virus ITR’s”: view ITR sequences if available (each set is shown in its own window)
“Fetch and view GenBank file”: view the Genbank file from the NCBI site
“Ortholog Group Details of virus”: view the ortholog groups associated with selected genomes
“Changes log”: view any changes that have been made to all genomes as well as the date the change was made
The Draw Menu
“Genome Map”: view the genome map for selected genomes
“Ortholog Group Map”: view the genome maps for 2 viruses in one window. Lines will connect any common ortholog groups
“Genes/ORFs grouped by strand”: view a graph showing the strand location of each gene. To find the location of gene “N” (where N is the gene number), calculate the slope using the points on the graph that represent gene “N” and gene “N-1”. A negative slope indicates the gene is located on the – strand; a positive slope indicates the gene is located on the + strand. Multiple genome plots may be displayed on the same graph.
For a more in-depth explanation of these features go to The Drawing Features section.
The Tools Menu
This menu provides direct access to all VBRC tools. Using this menu, you can open the following programs from within VOCs:
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- VGO
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- Base by Base
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- JDotter
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- DNA Grapher
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- Codon Statistics
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- Genome Comparison
Note: if a set of genomes has been selected (or de-selected using “Do NOT select these viruses”) from the Virus Selector prior to opening one of these tools, the tool will be applied to the current selection (or remaining selection) of genomes. If nothing has been selected from the Virus Selector, the tool will be applied to all genomes in the current database.
The Search Menu
“Genome sequence expression search”: enter a string of nucleotides to search for all genomes with that exact nucleotide pattern. If any genomes are selected within the Virus Selector, the search will only apply to the selected genomes.
“Genome sequence fuzzy search”: very similar to “Genome sequence expression search” except in addition, the number of mismatches may be defined. The number of permittable mismatches by VOCs is “n-1” where “n” is the number of nucleotides in the string entered in the search field.
The Export Menu
“Write … File”: write the DNA sequence of a selected genome to a file. The file format can be: GenBank, Fasta (protein also), GFF, XML (BSML), or EMBL format.
The Links Menu
“Manage bookmarks”: add or remove links to external webpages in this section of the menu bar.
“NCBI”: link to NCBI’s website
The DB Info Menu
“Database server and data information”: view statistics relevant to the current database
Window Menu
Drop down menu of all open windows
The Help Menu
Access online manuals and help pages
