SGD

SGD Help: Pairwise Chromosome Similarity View

Contents


Description

Pairwise Chromosome Similarity View allows you to examine similarity matrices within the yeast genome. This is accomplished by customizing a group of settings, and then clicking on the view itself in the location where you want to "zoom" in or out. Direct repeats are shown in blue and inverted are shown in green. Tick marks on the axes and corresponding grid lines on the image demarcate, in base pairs (bp), even multiples of the appropriate power of ten for orientation purposes.

These images are generated from static lists of similarities for each pair of chromosomes that were originally generated from the DNA sequences according to specific parameters. Details are available.

Using Pairwise Chromosome Similarity View

  1. Scrolling (left Margin)

     These buttons allow scrolling in the directions indicated. Each one scrolls the view by one-half screen.


  2. Region Displayed (left Margin)

     This graphic shows the position of the current view (colored gray) within the context of the entire similarity matrix (colored black). Initially, the entire box is gray indicating a fully zoomed out view. The axes are labeled with the chromosome numbers.


  3. Image Settings (left margin)

    You can change any of the image settings by pressing the button for the value desired. The current value for each setting is enclosed in brackets. The screen will redraw after each adjustment, even if the image itself doesn't change.

    1. Changing the Zoom Settings

      • Zoom Direction: This specifies whether you want you zoom in or out when you click on the image. Zooming in will increase the magnification; zooming out will decrease it.

      • Zoom Magnification This specifies the RELATIVE zoom magnification. In other words, it specifies how many times the image will be magnified or reduced by (depending on zoom direction) when you click on the image.

    2. Zooming

      Once the zoom settings have been adjusted according to preference, click the mouse button on the existing image at the location where you want to zoom in or out. This will then be the center for the next image. Obviously, zooming in is much more sensitive to mouse placement than zooming out. The closest you can zoom in is to a window 1k bp on a side.

      NOTE: You can use your browser's "BACK" button to return to a previous view and continue from there.

    3. Changing the Minimum Similarity Size

      The purpose of this control is to allow the user to filter out smaller similarities to quickly locate the more significant ones. The setting is a cutoff point in base pairs below which similarities are not displayed. The default is set to 30 bp because that weeds out a lot of distracting small similarity "noise." The lowest setting, 20 bp, displays everything available in the data set. To change the minimum size, press the button for the desired level.

    4. Changing the Image Size

      This specifies the largest dimension, in pixels, of the images generated when zooming in or out. This allows flexible sizing according to the viewers particular screen geometry. The default is 300 pixels. To change the image size, press the corresponding button.


  4. Other Options (upper margin)

    1. Pick Different Chromosomes: This link brings you back to the introductory screen and allows you to pick another chromsome pair to view.

    2. Zoom Completely Out: This link automatically zooms all the way out, showing the whole chromosome on each side.

    3. Tutorial: This link brings up a quick tutorial.

    4. Custom Re-Scan of Current View: This link appears when the view is approximately 2.5k bp or less on a side. It allows you to perform a scan similar to the one that generated the data that Pairwise Chromosome Similarity View uses to generate images, but with customized settings. This can be used to perform a more exhaustive scan of a particular area. These scans can take several minutes, so the button does not appear until the size of the area is sufficiently small. Follow the link for details.


  5. Feature Display (appears when sufficiently zoomed in):

    Colored bars, indicating where genetic features (ORFs, tRNAs, deltas, etc) are located on each chromosome, appear along the axes when the view is less than approximately 150k bp on a side. Labels identifying the features appear upon zooming farther in (approximately 28k bp on a side). Blue bars indicate Watson features and green bars indicate Crick features.

    At the same time, a small form will appear below the view, where you can select a sequence or visible feature, and then go to the Gene/Sequence Resources page with that sequence or feature by pressing "Go to Gene/Sequence Resources."

Accessing Pairwise Chromosome Similarity View

Pairwise Chromosome Similarity View can be accessed by:
  1. Going to the Genome-wide DNA Similarity View main page and then choosing a pair of chromosomes by clicking at the appropriate row and column
  2. Entering a sequence name or chromosome region in Gene/Sequence Resources and then chossing "Genomic Stripe View" as the display method. To go to Pairwise Chromosome Similarity View, click on the desired area of similarity where it appears on the black chromosome display.

Links to Other SGD Pages

Go to Genome-wide DNA Similarity View

Return to Saccharomyces Genome Database Send a Message to the SGD Curators