Understanding the Display

2.1.1. VISTA Graph Display

The central window of the browser contains several important blocks of information. The most visible of these are the VISTA graph panels, which show the so-called peaks and valleys graphs. These graphs represent percent conservation between aligned sequences at a given coordinate on the base sequence (see Note 1 for how the curve is calculated). Multiple pairwise alignments that share the base sequence can be displayed simultaneously, one under another. The percent identity bounds are shown to the right of every row. These bounds can be adjusted by clicking on the curve to select it, and then clicking the "Parameters" button. The graphs are numbered, you can identify each graph in the list underneath the VISTA panel.

2.1.2. Annotation

The browser shows the base genome annotation directly above the curves. Arrows signifying genes are drawn above the graphs, pointing in the direction of the gene. Exons and UTRs are marked on the gene as colored blocks. Gene names appear underneath the arrows. Repeats are shown directly above the plot, colored according to the legend in the lower left-hand corner of the display. The annotation can be changed in the control panel, as described in Subheading 2.2.1.

2.1.3. Conserved Regions

Regions of high conservation are colored according to the annotation as exons (dark blue), UTRs (light blue), or noncoding (pink). The thresholds of conservation that determine what gets colored, as well as minimum and maximum y-axis values, can be easily adjusted by right-clicking on the curve and selecting the "Parameters" option (see Note 2).

2.1.4. Contigs

The thick gray or red lines under the plot show where the second species was aligned to the base sequence. To find out the name of the contig or chromosome that was aligned, one can hover the mouse cursor over the graph—the name will be displayed in the information panel on the left. Red lines indicate that multiple regions from the second sequence were aligned to this base sequence location, and several alignments are overlapped here (see Note 3). Gray lines indicate an unambiguous alignment.

2.1.5 Location on the Base Sequence

At the very top of the central window there is a long bar representing the whole contig or chromosome that one is browsing. A moveable red rectangle on top of that bar represents the location of the region one is looking at on that contig or chromosome. The rectangle can be stretched or moved to change the location being browsed.

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