VISTA Track Help
Fig. 1. VISTA Track |
Fig 2. VISTA Track Controls |
Fig 3. Custom Track Link |
About
VISTA Track is a simulated custom track built on top of the UCSC genome browser. It displays the standard VISTA graphs above the picture from UCSC, and provides controls to adjust certain parameters.
This document provides help with the VISTA features only -- for help using the standard UCSC Genome Browser features, please see UCSC's help pages.
VISTA track display
The "peaks and valleys" graphs represent percent conservation between aligned sequences at a given coordinate on the base sequence (see how the curves are calculated). Multiple alignments that share the base sequence can be displayed simultaneously, one under another. The order of the curves can be changed by clicking on the up and down arrows next to the curves.
To add Custom Tracks, use the link at the bottom of the Vista Track page (Fig. 3).
Alignment Details
Underlying sequences, alignments, conserved regions, annotations, and other detailed information can be retrieved by clicking on the Vista picture. From the page that opens, the user can also submit small (20K) pieces of the alignment for rVista analysis.
Controls
Sliding Window
The sliding window parameter controls the size of the sliding window used to calculate the VISTA curve. Adjusting the sliding window affects all curves that are displayed.
Mode
For each "track" (an alignment of a sequence or sequences with the base genome), the user can select the mode in which this track is displayed. "Full" shows a graph of every alignment on a separate line (useful when examining areas where alignments overlap). "Dense" shows all of the graphs on the same line, taking the maximum conservation when overlaps occur. "Hide" stops the browser from displaying the curve at all.
Contigs
Checking the "Contigs" checkbox will cause gray lines to be drawn under the VISTA curves where a contig was mapped to the base genome
Conservation, Window
For each curve, parameters used to calculate conserved regions can be adjusted. These are the conservation and the window parameters. Conservation is the minimum percent identity that must occur in a region for it to be considered conserved. Window is the size of the sliding window used to calculate the conservation. More about how the curve is calculated can be found in VISTA Browser help.
Min Y
One can adjust the lowest conservation shown for each graph by changing the min y parameter, which is 50% by default.
