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JFreq How-To Documentation
Loading VOCS databases and genomes
Load one or more genomes from a VOCS database
Open the JFreq program. You may choose to search either all genomes of a particular virus family, or select specific genomes in which to carry out your search.
– To select all genes of a virus family (e.g. Coronaviridae), click in the circle to the left of “All genomes.” A list of virus families will open: choose “Coronaviridae”, then click Choose. The list of genomes will take a few moments to load.
– To select only selected genomes of a virus family (e.g. Coronaviridae), click in the circle to the left of “All genomes.” A list of virus families will open: choose “Coronaviridae”, then click Choose. The list of genomes will take a few moments to load. Choose one or more genomes of interest by holding down the CTRL key and selecting with the mouse.
You may now continue with your search (see below.)
Switch to a different VOCS database
Select “Choose Database” from the File menu. The database list will re-open; select your database of interest.
Load a user-supplied sequence
Click in the circle to the left of “Local file”. Select the file containing your genome(s) to be searched and click Open. You may now continue with your search (see below.)
Choose your search type
There are three types of searches you can perform using the selected genome(s):
– You can search for words with unusual frequencies (i.e. appearing more or less often than statistically expected.)
– You can search for words with unusual distributions (i.e. distributed unevenly throughout the genome.)
– You can search for all occurrences of a specific word (e.g. CTTAA).
Select the search you wish to perform from the panel to the upper left, than adjust parameters (if necessary) in the lower left panel. Click the red Search button to begin the search.
Adjust the cut-off Z score
The results table will only display rows that fall outside the lower – upper Z-score range shown above the table (default = -3, 3.) The number of rows that meet these criteria is given beneath the table (e.g. “56 of 5440 rows shown.”) (Note: the Z-score cut-off criteria will apply even if your table is currently displaying a statistic other than the Z-score (such as Std Dev). You can choose which statistic to display from the panel to the upper right of the Results Table.)
If you wish to adjust your Z-score criteria so that fewer or more rows are shown, you may do this by altering the Significance (Z-score) threshold shown above the table.
– The up or down arrows to the right of each box will adjust your Z-score threshold by increments of 1. The table will be automatically refreshed with each change.
– To adjust the Z-score in finer increments, click in the box itself and type your desired upper or lower Z-score. The table will not automatically be refreshed; press the Enter button on your keyboard to put the new parameters into effect, or click in the other box.
Generate a histogram for a genome
From the Result List, you can generate a histogram to show the distribution of word results in a specific genome. Click anywhere in the column containing results for the genome of interest, then click Histogram (above the Result Table). A histogram will automatically open showing word count vs. Z score for 0.3 Z intervals. (E.g. for ZEBOV-May_Russia, the frequency histogram shows that there are 550 words (of length = 3-6) falling in the 0.3 – 0.6 Z range.)
View search results graphically
To graphically view the distribution of a single word throughout the genome, select from the Results Table the word(s) of interest in a single genome column (e.g. GAT and TTTG in the ZEBOV); hold down the CTRL button to select multiple words. Click the Open in VGO button above the table.
The VGO program will then load, displaying the genome together with its start (green) and stop (red) codons. Occurrences of the word in question will be displayed above the genome as black boxes. Clicking on a box will cause its identity (e.g. TTTG) and position (e.g. 4147) to be displayed at the bottom of the VGO window.