Most of XPlasMap’s functions should be fairly obvious. This section is aimed at clarifying some less obvious points.
XPlasMap draws DNA maps: Circular DNA (e.g. plasmids) or linear DNA (e.g. genomic views). The maps can be annotated, fragments can be added or deleted to plan or match your cloning, and so on. XPlasMap can perform restriction mapping and open reading frame analysis, but only when importing a new sequence. The sequence is not saved after import, so you can’t make modifications to the map and then search for restriction sites. (There are several excellent free programs for Mac OSX that will do sequence analysis.)
There are generally several ways to do common actions. For example, a new gene can be added by (1) clicking on a menu item (“Features→ New Gene”); (2) typing ⌘-G; (3) clicking on the toolbar icon. Pre-existing genes can be edited by (1) selecting (highlighting) the gene and clicking a menu item (“Edit→ Edit selected”); (2) selecting the gene and typing ⌘-E; (3) double-clicking the gene; (4) using the contextual menu item for the gene; (5) double-clicking on the description of the gene in the “List View”.
Most features have a contextual menu (control-click, or right-click) that offers quick access to modifications, edits, or deletions.
Set various default values in the Preferences, including whether to look for open reading frames in imported sequences; how to identify open reading frames; favourite sets of restriction enzymes for mapping during import; and default fonts and exported image resolutions.
The List View (“Maps→ List View”, ⌘-L, or toolbar icon) is particularly useful for complicated maps with many features or restriction sites. List View shows all the features in a table view that can be sorted by start, end, type, etc. Features can be edited individually (select and double-click), or as a group (select several and double-click).
Dragging on a gene moves the text, not the gene itself. To move the gene itself, hold down the command (⌘) key and drag. To edit the shape of an arrow, oval, or rectangle, command-click (⌘-click) on it; a red cross-hair will appear at the “end” of the annotation. Drag the cross-hair to change the shape.
1. How can I save a DNA map as an image?
Export to PNG or JPG (File menu), then insert that image into whatever program you’re using. (For practical purposes, the main difference between Save as JPG and Save as PNG is that the JPGs have a solid background, the PNGs have a transparent background.) Or, go to the Print menu and Save As PDF.
2. How do I draw a map from a plain text file? From a FastA file?
Select “Import→from FastA or text” in the File menu, and select a file of the appropriate format.
3. What’s the advantage of drawing a map from a plain text or FastA file?
GenBank and EMBOSS files describe genes and other features, but FastA and text sequences, by default, will be imported as a blank map of the appropriate size, as if you had just entered the size in Maps→New Linear DNA. The advantage is that you can map open reading frames and restriction enzymes on import. (Note that the sequence is not saved, so after the map is imported you can’t go back and find more restriction sites or open reading frames.)
4. How do I draw a map from a GenBank file?
First, go to GenBank, find your sequence of interest, and select “GenBank (Full)”, and “Send to File” to save the sequence to your drive. Then select “Import / from GenBank (.gb format)” in the File menu, and select the file. You’ll be asked which of the features you want to display on your map. (The features can be sorted in various way, and you can limit the features that are shown to only include the kind you’re interested in.) Check them off, and you’re done, though you may need to edit some points.
5. My gene of interest doesn’t have its genomic information in GenBank.
If the organism has had its genome sequenced, even if you don’t easily find an individual file for your gene, you can usually readily find a longer stretch of DNA containing your gene of interest, even if it may have many other features as well as the one you want. Download the long stretch (make sure you select GeneBank (full)). Make a map from that, copy the region that contains your gene, and make a new linear map from the copied region (just select “New linear DNA”, and tick the checkbox for “Make linear map from copied fragment”. (If the stretch of DNA you originally downloaded has many features and it’s hard to identify your gene, use “List view” to quickly limit and sort the features and find the start and end positions of the gene.)
If the genome hasn’t been sequenced, you’re on your own.
6. What’s the advantage of drawing a map from a GenBank file?
The map will include any of the features listed in the GenBank files that you want to import. You can map entire chromosomes this way (though it takes a minute or so, and the results often look pretty cluttered).
7. What’s the “List view” for?
List view (in the Maps menu) shows all the maps’ features in text form. If you’ve turned off display of a feature on the map view, the List view is the only way you can edit it to turn it back on. As well, because you can limit the List view display to one kind of feature and sort by position, name, kind, etc, you can sort restriction sites etc. in various ways. Having sorted, you can also edit groups of features as a batch.
8. What are the different gene styles for?
With circular maps, there’s only one basic gene style (“Simple”), an arc with or without an arrow, although you can vary many aspects of the arc (presence, absence, direction of arrow; location of arc relative to plasmid backbone; color; text color; text position). Linear DNA maps are more likely to show genomic views, and so there are two additional gene styles available in Linear view: “Exons” and “Hybrid”. These styles are very similar to each other: Both show a gene as a series of exons (if the information is available). “Exons” style indicates the orientation of the gene by making the last exon an arrow; “Hybrid” style draws an arrow underneath or above the gene, to indicate the orientation. “Exons” view is a little less cluttered, but when the exons are small (e.g. when a long stretch of DNA is being mapped) the arrows are hard to see. “Simple” view makes gene location clearer. “Hybrid” view shows exons, and makes gene orientation easier to see, but also makes the view a little more cluttered.
9. How do I enter and edit exons in a gene?
The simple way is to import the genomic view from GenBank. XPlasMap will pick the exon info from the .gb file.
The other way to enter exon info is by hand. Enter a new gene, if necessary. It will be shown as a “Simple” style, no matter what style you choose in the New Gene dialog, because there’s no exon information. Now select “Exons” from the gene’s contextual menu. This opens a form where you can enter exon information. Enter the start and end of each exon relative to the gene start, not to the overall map, and ignore gene orientation: If gene starts at 1000 bp on the map, and the third exon starts at 6000 on the map, then enter 5000 (the distance from the gene start) as the exon’s start.. After your exon info is entered, make sure the gene style is either “Exons” or “Hybrid” to see the exons. (Remember that only linear maps accept these styles.)
10. What are the different multiple cloning site styles for?
The three different MCS styles are purely for show, they don’t indicate anything functional about the MCS. “Arc” style (especially for circular maps) look good (at least to me) unless there are a lot of enzymes listed, when “Boxed” or “Text” style is less cluttered.
11. I turned off display of an enzyme (or gene, or MCS). How can I edit it to show it again?
Normally, to edit a feature you double-click it on the Map view. Obviously, if you’ve turned off display of the feature, you can’t do that. Use List View (Maps→List View) to reveal all features in a sortable text view, and double-click the feature to get the edit dialog again.
12. How do I change the font?
Change the default font in the Preferences menu. To change the font for individual items, highlight the item and Edit→Set Font. To change the font for, e.g. all genes or all enzymes, make sure no feature is highlighted, and click Edit→Set font.
13. How do I restriction-map my DNA?
When you import from a DNA file (FastA, text, or GenBank) select an enzyme set from the “Enzymes” pull-down menu. Be aware that mapping a large piece of DNA (megabases) will take a minute or two.
14. How can I map with just the enzymes I’m interested in?
In Preferences, “Select Enzyme Set”. You can choose enzymes and give the set a name. Next time you import DNA, that set will be an option. (The default enzyme sets offer enzymes that cut once or twice, as well as 6 and 8-cutters.)
15. How I can identify restriction sites after I’ve already imported a DNA sequence?
At least for now, you can’t. Sequence information isn’t kept after the map is drawn. You would have to import again.
16. How do I map open reading frames?
Make sure the “Identify ORFs” option is checked in the import dialog. Set the definition of an ORF (length, etc) in Preferences.
17. How do I ... ?
If there’s a feature you want added, something you can’t figure out, or (especially) if you find a bug, please send email to email@example.com.