Most of the spin functions display their results in a two-dimensional plot called a "spin plot" ( see section SPIN Sequence Plot). Sets of matches from a single invocation of a function 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 figure shown below shows a spin plot window containing the results of a gene search method based on codon usage, superimposed on a search for stop codons ( see section Codon usage method). Each plot window contains a cross hair. Its x position is shown in sequence base numbers in the left hand box above the plot, and the y coordinate, expressed using the score values of the gene search, is shown in the right hand box.
At the right hand side of each panel is a set of square boxes with the
same colours as the lines drawn in the adjacent plot. These
icon-like objects represent individual results and allow the user to
operate on them. For example at the right of the middle panel is a
pop-up menu containing the items: "Information", "List results",
"Configure", "Hide" and "Remove".
(
see section Result manager).
These icons can also be used to
drag and drop the results to which they correspond. This is activated by
pressing the middle mouse button, or Alt left mouse button,
over the box and then moving the cursor
over the spin plot to the new location or anywhere outside the spin plot
(
see section Drag and drop)
Each spin plot window also contains a cursor that denotes the position of
the cursor in the Sequence display window
(
see section Sequence display).
The user can move a cursor by clicking and dragging
with the middle mouse button, or Alt left mouse button.
This will move the cursor in the sequence display and all other cursors displayed
that relate to the sequence.
The graphical results can be zoomed and scrolled in both x and y
directions. Zooming is achieved using the X and Y scale bars at the top
left hand corner of the plot. The individual plots can be scrolled in y
using the scroll bars attached to their right hand edge. The sequence
can be scrolled using the scroll bar at the base of the plot.
To illustrate further uses of the program we include some more screen
dumps below.
The figure above shows the results of a search for restriction enzymes
(
see section Restriction enzyme search).
The figure above is a plot of the base composition of a sequence.
The figure above shows the way in which the results of
weight matrix searches for motifs are plotted
(
see section Motif search).
The figure about shows the way in which the results of
searches for splice junctions are plotted. The donor and acceptor
predictions are separated and a different colour is used for each
reading frame
(
see section Splice site search).
The figure above shows a method for finding protein coding regions which
does not distinguish reading frame or strand
(
see section Uneven positional base preferences).
The figure above shows how results from the tRNA gene search function
are displayed in the Output window
(
see section tRNA search).
![[picture]](spin_plot_p.unix.gif.html)
(Click for full size image)
![[picture]](spin_restrict_enzymes_p.unix.gif.html)
(Click for full size image)
![[picture]](spin_plot_base_comp_p.unix.gif.html)
(Click for full size image)
![[picture]](spin_weight_matrix.unix.gif.html)
(Click for full size image)
![[picture]](spin_splice.unix.gif.html)
(Click for full size image)
![[picture]](spin_base_bias_p.unix.gif.html)
(Click for full size image)
![[picture]](spin_trna_t.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_5.html