DNAMAN provides convenient tools to produce publication-quality restriction maps. These tools can be used to draw linear or circular restriction maps. You may also use this drawing tool for other projects, such as PCR strategy diagrams, gene structural maps, etc.
There are two accesses to draw a restriction map:
1. Use the Restriction | Draw Map command if DNA sequence is not available. A plasmid map will be drawn immediately in a Restriction Map window. Since sequence information is not available, there is no sequence associated with the map. You may double-click in the window to modify the properties of the map.
2. If DNA sequence is available, you can draw a restriction map according to the data from restriction analysis. Choose the Restriction | Restriction Analysis command and select Restriction Map option to start drawing the restriction map. There is a DNA sequence associated with the map. Any modification of DNA fragment on the map may result in the change of sequence.
By double-clicking the map window, a dialogue box will appear for modification of the map properties.
The first page contains general information about the restriction map. You may define the name and the size of the map. You may also change the type of the map to linear or circular.
There are two parameters to define the location and the size of the map;
1) Map frame.
The size of a plasmid circle, or the length of a linear fragment, is defined by map Diameter. The value is in logical point units that are based on your screen resolution. The Size (thickness) of the frame is also in logical point units.
2) Map center position.
The center is defined as X position, from left to right of the screen, and Y position, from top to bottom. The unit is in logical point as well.
There are three options to change the appearance of the map:
1) Show scale of linear map. This option applies only to linear map. If checked, DNAMAN will draw a scale to show the length unit of the linear Map
2) Show end positions. This option applies to both linear and circular map. In a linear map, the start and end positions are labeled if this option is checked. In a circular map, the top position will show up when this option is checked.
3)Show enzyme position in new site(s). If this option is checked, DNAMAN will display the restriction sites together with their positions when they are added to the map.
This page contains also reference information about the map. You should enter the Author of the map and other relative information such as description.
The second page contains the list of elements in the map. From this page, you may add new element(s), modify or remove existing elements. The Name button allows you to link an element to an available text object in the map.
The third page contains the list of text objects in the map. From this page, you may add new text object(s), modify or remove existing text objects.
The fourth page contains the list of sites in the map. From this page, you can add new restriction site(s), modify or remove existing sites.
If the map contains DNA sequence, the fifth page shows the information about Sequence View. In this page:
DNAMAN provides the following methods for drawing maps:
1. Adding a site
1) Place the cursor to the desired position on the map (the coordinate is displayed on the left corner of the screen). If the enzyme site is within an element, you should first move the element out of the map frame (inward or outward in a circular map, up or down in a linear map).
2) When the cursor is a cross, click to display a popup menu.
3) Select the Add Site command to open the New Site dialog box.
4) Type the site name. You may also define the position number in the position box.
2. Adding an element
Click on the map frame to display a popup menu.
Clicking the Add Element menu opens the Element dialog box. You should fill in the five parameters (type, start position, end position, size and color) to create the element.
Arrow element is directional. Direct the arrow to clockwise or from left to right by entering the numbers in ascending in the Start (bp) and the End (bp) columns (e.g., Amp element from 3000 to 3500). You may reverse the arrow for anti-clockwise or from right to left by entering the number in descending (e.g., Lac element from 2800 to 2300).
Bar element is not directional and you can enter the numbers in either way.
To draw an element crossing the position +1 of a circular map, the end position should be the real position plus the size of the plasmid. For example, the Promoter A is from +4200 to +50, therefore, type 4200 in the box of Start (bp) column and 4350 in the box of the End (bp) column that is sum of 50 plus the size of the plasmid 4300.
Eight colors (patterns) are listed in the Color column of the dialog box:
3. Adding a Text object
Choose the Edit | Add | Text command to open the Text dialog box. Type the text in the edit box. You may change the font, style, size and color of the text by clicking the Font button. Choose the Vertical option if you like the text to be drawn vertically. After clicking the OK button, the text object will be added in the map.
4. Removing or editing a site
1)Double-click on the site name.
2)Delete the name in the edit box for removing the site, or modify the name for editing.
If you want remove more than one site, use mouse to select all of them, then choose the Edit | Delete menu to remove all.
5. Removing or editing an element
1)Double-click on the element.
2)Select a NULL type to delete the element, or modify the parameters for editing.
6. Removing or editing a Text object
1)Double-click on the Text object.
2)Delete the name in the edit box for removing the Text object, or modify the text or font for editing.
7. Moving a site name, an element or a Text object
Place the cursor on the object, then drag and drop it to an appropriate position.
8. Text alignment
You may align Text objects and site names in four directions and arrange them horizontally or vertically with a defined interval.
1)Press the left mouse button to select the Text objects and site names. There are six commands activated in the Edit menu.
2)Select the Edit | Object Align Left command to align the objects to the left.
Select the Edit | Object Align Right command to align the objects to the right.
Select the Edit | Object Align Top command to align the objects along the top.
Select the Edit | Object Align Bottom command to align the objects along the bottom.
3)-Select the Edit | Object Align As Column command to open the Column box where type a number to set up the vertical alignment interval.
Select the Edit | Object Align As Row command to open a dialog box where type a number to set up the horizontally alignment interval.
9. Changing text fonts
Double-clicking a text object to open the Text dialog box. Clicking the Font button, then select an appropriate font, size style and color and click OK.
You can also select a group of text objects, then change the font. There is an option to display the text horizontally or vertically.
10. Inserting or removing a fragment
1)Place the cursor in the position where you want to insert or delete a fragment.
2)Click the cross shape cursor to display a popup menu.
3)Select the Insert Fragment command to add a fragment in the map. If you want to delete a fragment choose the Remove Fragment command.
4)In the Add Fragment dialog box, you can change the inserting position by typing another number.
In the Remove Fragment dialog box, type in the start and the end positions of the fragment you want to be removed.
5) Click OK to continue.
11. Copying and cutting a fragment
1) Place the cursor in the approximate position where you want to copy or cut a fragment.
2) Click the cross shape cursor to display a menu.
3) Select the Copy Fragment command to copy a fragment to the Clipboard. If you want cut a fragment and place it into Clipboard, choose the Cut Fragment command.
4) In the Fragment Positions dialog box, type in the start and the end positions of the fragment you want to copy or cut.
5) Click OK. The defined fragment will be copied or cut into the Clipboard.
12. Pasting a DNA fragment
Be sure a fragment has been copied or cut into the Clipboard.
1) Place the cursor in the approximate position where you want to insert or delete a fragment.
2) Click the cross shape cursor to display a menu.
3) Select the Paste Fragment or Paste in Reverse Direction command.
4) In the Paste Fragment dialog box, you can change the position by typing another number.
5) Click OK.
If you paste a DNA fragment with sequence to a map without sequence, the sequence in the fragment will be ignored. If you paste a DNA fragment without sequence to a map containing sequence, DNAMAN will ask if you want to insert “N”s in the map sequence, or remove existing map sequence.
13. Adjusting the scale of a linear map
Double-clicking on the text of the scale to open a dialog box. You may change the scale by typing an appropriate number and clicking OK.
14. Resizing a map
You may increase and decrease the length of a linear map by placing the cursor to the right end of the map, then pressing the left mouse button. When the cursor switches to a small square, drag it to left or right to make adjustments to the map.
The size of a circular map can also be enlarged or reduced by placing the cursor to the circle of the map (not on an element). When the cursor is a cross, press the left mouse button and then make adjustments by moving the cross cursor inward or outward.
15. Moving a map
You can move the restriction map within the graphic window. Place the cursor in the center of a circular restriction map, or the left end of a linear map, then press the left mouse button, and drag and drop the map to the desired place.
16. Rotating and opening circular restriction map
DNAMAN allows you to rotate the restriction map. There are two methods.
Method 1:
Check the Show end position option when setting map properties, the top position appears on the map. Double-click this number to open the Text dialog box and type a new number to rotate the restriction map.
Method 2:
1)Check the Show end position option when setting map properties, the top position appears on the map. When you move the cursor under or above this number, the cursor switches to the shape.
2)Press and keep the mouse button down to rotate the restriction map.
When you draw a cloning diagram, you may want to illustrate the insertion on a restriction map. DNAMAN allows you to open the circular restriction map.
1)Place the cursor above the center of a circular restriction map and the cursor then switches to the shape. If you want to open the circular map at a position rather than at +1, you should first rotate the desired position to the “top” position.
2)Press and keep the mouse button down to open the restriction map. If you want to open it wider or narrower, place the cursor to an end and then press the left mouse button.
Note that the action of resizing, rotating or opening a restriction map results in the recalculation of the site positions.
17. Editing Sequence
If the sequence is available in the map, you may modify it with editing functions, e.g. insertion and deletion of bases, sequences. Copy and Paste may also be used. The map will be automatically updated when you make any modification of the sequence.
If you paste a DNA fragment containing sequence to a map without sequence, the sequence in the pasted fragment will be ignored. If you paste a fragment without sequence to a map containing sequence, DNAMAN will ask you if the letter N should be added to the map or all sequence in the map should be removed.
DNAMAN provides a useful function to manage the map files. It is recommended to store all map files in a designated folder. The default folder is "seqmap" in the DNAMAN folder. All map files in this folder will be displayed when you choose the Restriction | Restriction Map Files command.
In the Map File List dialog box, you may find the information in any map file by clicking the file in the list box. DNAMAN shows the map name, map length, and the type of the map (Linear or Circular). DNAMAN shows also the author and description of the map. The number of restriction sites, elements and text objects are also displayed.
You may highlight a map file and click the Open button to open the file in DNAMAN. You may also list the information of all map files by clicking the Show All button. The content of the list may be printed out using the File | Print command.