## Feature-map

[see also Help for DNA Analysis window]

This display represents the the sequence. You can pick most things.

### Genefinder

Much of the functionality of Phil Green's genefinder package is built into ACEDB. A reference is given when you first use the package. To access genefinder functions, use the right mouse button on the indicated box to get at the submenu. You must get "Genefinder features" first. Then "Autofind Gene" will act in the current active zone. It will attempt to find the best predicted gene including all features currently selected (indicated in LIGHTGREEN). If you have write access it will create a working gene model, called "Temp_gene". Selected features can be hand-edited by using the submenu attached to each feature. "Fix temp_gene" allows you to make temp_gene into a permanently stored gene prediction. "Gene -> selected" allows you to set the selected features from a previously determined gene. "Selected -> temp_gene" lets you convert the currently selected features into a gene structure. One common cause of problems is that some features are selected somewhere else in the sequence (perhaps the other strand!) -- use the "Clear" button to reset everything.

Genefinder uses tables of codons frequencies etc which are part of the acedb distribution in the wgf subdirectory. The environment variable GF_TABLES will overide the $ACEDB/wgf default and let you use your own tables.

### Display Control Button

This gives access to a menu of display options. All the options can be toggled by picking on them. e.g. select "DNA Sequence" to see the DNA. Note that, to see the DNA, you should zoom in quite a lot. Otherwise the bits of sequence ends with ... on each line.

### 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: insure that the next gmap will be displayed in a different window, otherwise the present one will be reused.
- Clear DNA: Uncolors the DNA
- Hide Header: Hides the buttons etc, useful before printing. The pop up menu remains available to toggle back.
- Color exons: Shows the exons on the DNA sequence if present.
- Export translation: Export the translation of the active gene as an Ascii file in Fasta format
- Export translations: Export the translation of all the genes of the active map in a single file in Fasta format
- Export Sequence: Export the active DNA zone in fasta format.
- Statistics: Prints on the console some statistics on genes, exons etc.
- Analysis window: opens a new window called DNA Analysis with its own help entry.

### Top Line

The last sequence you touched is the Selected fMap, this shows in red in the top left corner. This is the sequence used by dna analysis and gels. You can have several sequence on the screen if you use the Preserve option in the menu.

### Zooming

The Zooming works as in the genetic map. It is controlled by the 3 buttons, whole (for when you are lost!), zoom in, zoom out, and the middle mouse button: to recentre slowly if the mouse is right of the scale bar, or recenter fast and zoom continuously by dragging the mid button starting left of the scale bar.

### Active-Zone and Origin

You can reset the origin by picking the origin value box, typing a number and RETURN. Alternatively, pick the Origin button then a gene.

The active zone, indicated in the same coordinate system limits the scope of the Anaylsis window, Genefinder, Fasta Dumps etc. It then shows as blue Shutter on the left side of the yellow bar.

### Clear

Clears the colourings, genefinder selections etc.

### Reverse-Complement

Pick it with the left button to reverse complement the sequence. But if you press the right mouse button, you get a sub-menu that lets you independently complement or reverse the sequence. This may be useful to compare the features of both strands. On the top right corner of the window, the staus REVERSED or COMPLEMENT is recalled.

Introns-exons are shown as rectangular boxes (the exons) connected by springs, the introns. The one on the right go downwards, the one on the left of the scale go upwards, i.e. they belong to the other strand. They correspond to the negative reading frames of the analysis menu.

Picking the subsequences move you to their text value.

Picking the clone box which may occur at the top will move you to the physical map.

In the case of cDna you will get a text hybridize to Yacs..., picking one of these yacs will put you on the physical map.

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last edited: July 1994