Agarose-Gels

## 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.

to Table of Contents

last edited: July 1994