Extracting Detailed Information

Once you have found regions you are particularly interested in, you may want to see the coordinates of conserved regions, their sequences, their underlying alignments and annotations, and other detailed information. All these data can be easily accessed by right-clicking on a curve and selecting the "Details" option or by clicking the "i" button on the toolbar. A new browser window will open (see Note 4), which shows detailed information about all the underlying alignments that form the curve you are looking at (Fig. 2). The detailed view is also referred to as Text Browser.

At the top of the Text Browser page there is a banner that displays the names of the aligned organisms. The sequence listed in the darker header area is acting as base. This banner also lists the program used to align your sequences. In some cases, a pairwise alignment might be part of a multiple alignment, in which case the rest of the organisms will be present here as well.

Underneath the top banner there is the navigation area, which shows the coordinates of the currently displayed region and offers a link back to the VISTA Browser and a link to a list of all conserved regions found. When available, there will also be a link to something called "VISTA Tracks," which are VISTA curves, like the ones you see in the browser, integrated into the University of California at Santa Cruz (UCSC) Genome Browser. This tool can be very useful, since the UCSC browser has many additional annotation tracks and features. Links to other outside browsers may also appear here. In addition, if Shuffle-Lagan (see the description in Subheading 4) was used as the alignment program, there will be a link to download dot-plots of the alignments produced.

The main table follows, which lists each alignment that was generated for the base organism. Each row is a separate alignment. Each column, except the last one, refers to the sequences that participate in the alignment. The last column contains information pertaining to the alignment as a whole. The first cell of each row also contains a preview of the VISTA plot of this particular alignment, which allows one to quickly evaluate the quality of this alignment and to see alignment overlaps.

By looking at a row in this table, you can see which genomic interval of each organism aligned to which. The "Sequence" links will return a FASTA-format-ted segment that participates in the alignment. Clicking on the "VISTA Browser" links will launch the VISTA browser with the associated species as the base.

The last column provides links to the alignments in human-readable and MFA (multi-FASTA alignment) formats, a list of conserved regions from this alignment alone, and links to pdf plots of this alignment alone. If the region being examined is 20 Kbp or shorter, rVISTA analysis can be performed, and a link to rVISTA will also be displayed here. You will notice that when the conserved regions are displayed, their lengths are actually web links. Clicking on them will pull up the conserved sequences from both of the participating organisms.

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