When a comparison function has been run on a pair of sequences a SPIN Sequence Comparison Plot will appear. The results from each comparison can be viewed in a "Sequence Comparison Display" in which the two sequences can be scrolled passed one another.
The SPIN Sequence Comparison Plot display shows the results of comparison algorithms. Each match is represented as either a single dot ("Find similar spans", "Find best diagonals") or a line ("Find matching words", "Align sequences", "Local alignment"). Sets of matches from a single invocation of a comparison command are termed "a result". Each result is plotted using a single colour which can be configured via the results manager ( see section Result manager). The maximum dimensions of the SPIN Sequence Comparison Plot are indicated on the rulers at the bottom and left hand side. It is possible within spin to compare many different sequences. This means that there may be more than one horizontal or vertical sequence shown in the spin plot. All the points are scaled to the largest sequence in each direction. Plots can also be extracted from or added to each SPIN Sequence Comparison Plot.
The diagram above shows the results of a "find similar spans" search (olive)
(
see section Finding Similar Spans),
and a "find
matching words"
(red) (
see section Finding Matching Words), between human and
mouse properdin (hsproperd and mmproper).
At the right hand side is a set of square boxes with the
same colours as the dots drawn in the adjacent plot. These
icon-like objects represent individual results and allow the user to
operate on them. For example, in the figure above, the user has clicked
the right mouse button on the icon to raise a pop-up menu beneath the
"matching words" result
(
see section Result manager).
The square icons can also be used to move the corresponding results to
new locations. These operations are explained below
(
see section Drag and drop).
The SPIN Sequence Comparison Plot has 3 menus, "File", "View" and "Results".
The "File" menu contains the "Exit" command to quit the SPIN Sequence Comparison Plot. This
shuts down the SPIN Sequence Comparison Plot display removes all the results displayed in that
plot.
The "View" menu contains the "Results manager" command, see
section Result manager.
The "Results" menu provides a quick method of interfacing with the menu
obtainable via the "Results manager" (
see section Result manager).
![[picture]](spin_dot_plot.unix.gif.html)
(Click for full size image)
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Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/spin_unix_44.html