Agarose Gels Display
When a sequence is available in acedb, this display will compute the
restriction pattern that you would obtain by cutting the sequence with
restriction enzymes. The result is shown as a simulated gel. A related
display (Gel-Pattern) compares and
displays restriction patterns entered as band lengths or migration
distances even if the sequence itself is not known.
To use the Agarose Gel Display, type in the name of a restriction
enzyme or a short sequence. Ambiguous bases like n, w, s etc are
reconised (see help on DNA_nomenclature). The
sequence being analyzed will correspond to the one in the active DNA
window. If you click a band, you light the corresponding part of the
sequence and the overlapping bands in the other lanes of the same gel.
The distance is a log funtion of the lenght of the dna-segment as
given in:
Sambrook, Fritsch, and Maniatis. "Molecular Cloning, a Laboratory
Manual". Second ed., Cold Spring Harbor laboratory Press, 1989. Figure
6.1, page 65
where
distance = 3.5 * ( 4 - log10(length) )
Menu items:
- Quit: destroys the window.
- Help: displays this help page.
- Print: prepares a Post Script file xxx.PS in ./PS.
You can then print it on your local laser printer.
Zooming
Zooming buttons works as in the genetic map. Whole
shows the whole gel, i.e. all the bands; zoom in, zoom
out change magnification. The middle mouse
button recentres display (if pointer is right of scale
bar). The same button is used to recenter quickly and zoom
continuously by dragging (starting with pointer left of the scale
bar).
Other Buttons
The coordinate button is a toggle that prints its length directly
above each band, in base pairs.
We hope to introduce soon other commands to add or remove a site
at a given place.
Picking a Band
If you click once on a band, its exact length is shown in the left
top yellow 'Position' box.
If you click again, you will color the corresponding region on the
sequence display. If the sequence is no longer the one used to produce
the gel band, the program is suppose to realise it, but we have not
tested all possible cases. At the same time, you will color the
matching bands in the other lanes. To restore normal colors,
select the same digestion box and type Enter.
More on Digestions
To perform a digestion, select a sequence window, select the origin
and length of the bit of sequence you wish to digest. Then pick one of
the text boxes top right in the Gel display. It turns yellow. Type in
your restriction enzyme names or short sequences. Separate multiple
enzymes or sequences by semicolons to create multienzyme digests. Then
type return. Typographical errors will display the help page on the
genetic code.
As many lanes as you wish can be displayed. The window resizes
properly. Different lanes may correspond to different sequences, but
then we are not to sure that the recoloring trick is bug free. So you
may have to clear the display from time to time.
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last edited: July 1994