## Clone-Grid

This display is designed to display hybridisation data from the YAC polytene filters (and other gridded filters), and provide a tool for people to go between such data and the map, even when they don't have write access to the database.

You see a set of squares layed out in the same pattern as the clones on the filter. To help orient you, the rectangle at left containing LABEL corresponds to where the numerical label is written on the filter.

The current active box (after you have clicked once in a box) has a cross in it and is outlined in red. The name of the corresponding YAC is shown in the Gridded Clone text entry box at the top. If you click on this to make it yellow, and type in the name of a YAC on the grid, that will be indicated with a cross/outlined in red. You can also click on the Gridded Clone button, in which case you can pick on YAC's elsewhere, such as in a physical map window. This is useful for finding where neighbouring YAC's on the map are on the grid.

There are two modes: Edit Mode and Map Mode. The mode with the coloured box is current. You can switch by picking the other box.

### Map Mode

When you click twice on a box you go to the physical map. If it is an empty box, then you will go to the corresponding YAC. If it is filled then it, and all the other filled boxes representing YACs that overlap, are highlighted in red, and you go to the average position on the map that they define. i.e. if a number of boxes are filled (positive) then map mode splits them into groups, each of which corresponds to one potential map locus.

The grouping is done by taking all YAC's within some range into a cluster. This range is 20 by default. It can be changed with the menu entry Set Cluster Range.

### Edit mode

This lets you define a pattern. Click with the left mouse. One click in a box gives a dark blue fill, a second makes it pale blue (signifying a weak signal), and a third will clear it.

### Probes

We now recognize two sorts of probes: simple clones and pools. Pools can contain collections of clone probes and subpools. The hybridisation pattern for a pool is the union of the patterns for all its clones and subpools, together with any data attached specifically to itself. You can type the name of a probe into the text entry box (after activating it to yellow by clicking on it) or you can press the Probe button and pick your probe from another window (e.g. a physical map window).

The Clear button clears any current pattern, deletes a clone name if ones is present, puts you in edit mode, and prepares the "Pattern for clone" entry box for you to type in a clone name. This does not affect any pattern stored as a "surround" for comparison (see below).

The arrow keys also work to let you move the active box (outlined in red) around the grid. Hitting the return key corresponds to clicking on the current active box.

### Menu items:

- Quit: quits the window.
- Help: brings up this help.
- Print: prepares a Post Script file in ./PS which you can then print on your local laser printer.
- Preserve: as in the phsyical map display. If you select POLY1 again after choosing this option then you get a new window, rather than reusing this one.
- Center <-> Surround: this places the current pattern in a surround to each highlighted box. You can then load a new pattern and compare it to the one stored in the surround. The clear function only affects the central pattern, not the surround, so to clear the surround select Center <-> Surround then Clear.
- Names: shows YAC names at all locations, rather than square boxes. To see the ones at the right you will have to stretch the box very wide (sorry no scrolling yet). If you print when stretched out you get an index sheet for the filter like the one sent out with it.
- Display probe as tree: shows the current probe in a separate window in tree (plain text) form.
- Save data with probe: only valid if you have write access and are entering hybridisation data for probes. This lets you save the current pattern with the probe whose name is in the Probe text entry box. Data that is set as weak (light blue) will be saved with "Weak" following the YAC name. When reading in data, if any text is found following the clone name the box will be displayed in light blue, so you could edit this text in a tree update window to be more informative if you wanted.
- Set cluster range: This value is used to cluster individual hybridizing YAC's into groups that are supposed to correspond to individual loci. The current algorithm essentially tries to find loci such that the centres of all the positive YAC's are within the defined range. This is not strictly correct. The units are physical map bands. Larger values allow more spread out clusters.
- Stats on KeySet: Applies to current keyset, which should contain probes with hybridisation data. It returns stats on how many clusters of various sorts there are, as a line on the terminal.
- Change Gridded Clone: doesn't do anything yet.

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last edited: July 1994