SGD Help: Genomic Stripe View
Contents
The Genomic Stripe View provides a way to display all the regions in
the genome that are similar to a selected sequence. The similarities
that are displayed are derived from a set of 256 pre-calculated
similarity matrices that compare every yeast chromosome to every yeast
chromosome. These matrices are the ones used to create the Pairwise Chromosome Similarity View. To learn more about the way the similarity
matrices are calculated, see Similarity
Data Generation Details.
- The Genomic Stripe View Display:
The Genomic Stripe View display is a set of sixteen black vertical
bars, or stripes, representing the sixteen S. cerevisiae
chromosomes. They are labelled at the top of the figure, and the
scale (in basepairs) is indicated on the left of the figure.
Similarities that are at least 25 or 30 base pairs long (depending on the length of sequence used) are indicated as
blue or green dots or lines. A blue line indicates that the
similarity is is in the direct orientation (when the sequences are
lined up from the left arm of the chromosome) and a green line
indicates that the similarity is in the indirect orientation. To
conserve space in the display, the vertical scale may be compressed
relative to that of the horizontal scale. This makes the patterns
slightly distorted, but using the Pairwise Chromosome Similarity View (see below)
will show you the uncompressed comparison.
- Connecting to the Pairwise Chromosome Similarity View:
Clicking on any part of an image in the figure will show you the
Pairwise Chromosome Similarity View for that part of the sequence comparison
matrix. Some of the advantages of displaying the Genome-wide DNA Similarity
View are that you can zoom in or out, scroll to see a different
section of the comparison, or even change the comparison parameters
(when the view is zoomed in to the full extent) using "Custom Re-Scan
of Current View."
Use Gene/Sequence Resources
to select a sequence to display using Genomic Stripe View.
Simply input the sequence for which you want to view similarities and
select Genomic Stripe View as the display option. Note that Genomic
Stripe View requires a minimum of 3,000 and a maximum of 100,000 base
pairs for the display. If your input sequence is smaller than that,
the program will add enough neighboring sequence to make 3000 base
pairs. If you enter more than 100,000 base pairs, the program will
truncate your sequence. The resulting display will be a graphical
representation of sequences throughout the genome that display
similarity to your input sequence.
Go to Gene/Sequence Resources
Return to Saccharomyces Genome Database