Savage Plasmids

I miss MacPlasmap, the Mac-Classic plasmid drawing program. I couldn't find anything that drew maps I liked, so I've written this web-based program. It generates plasmid maps you can view on your browser, as well as maps you can download and print, or view on your computer.

You'll need an SVG-capable browser to see the browser version; Adobe makes a free plugin for most browsers. Another option is to copy the source and view it with an SVG viewer, such as Batik, which can also convert SVG files to JPEG, PNG, or GIF.

Dec. '05 Firefox 1.5 renders SVG, but incompletely; the textpath element isn't rendered. Jan '06 Camino 1.0b2 also seems to have a problem with textpath.That means that much of the labeling of the plasmid maps won't show up in those versions of Firefox or Camino. Sorry. Hopefully a fuller set of SVG will be implemented soon. In any case, the postscript version shouldn't be affected by this.

The printable version is in Postscript format. On MacOSX 10.4 ("Tiger") this can be opened directly by Preview.app, which can convert it into various other formats, including PDF, TIFF, JPEG, and PNG. If believe (but haven't tested) that Postscript files can be readily interpreted on most other platforms.

This is hosted on my account, and for now, the files are saved in my account, but that's not likely to last if there's any significant use of this program. I'll worry about alternatives if it proves necessary. This program is freeware. I make no promises that it will remain freeware forever, but have no plans to charge at the moment.

I am contemplating making a standalone version, but that will have to wait until I find more spare time.

Feedback? Questions? Feature requests? Mail me.

Help

(In progress)

Some quick notes:

• Once you've drawn a plasmid once (either Postscript or SVG) the data are saved in a ".svp" file and can be loaded for further work.
• (New and experimental) "Insert/Delete" also allows fragments of plasmids to be saved, along with the features, restriction sites, etc in that section, and then inserted into other plasmids: "Virtual cloning".
  You will probably still need to tidy up the insertion manually:
• Restriction sites should present no problems.
• Features/genes will be included even if they were only partially included in the fragment.
• Multiple cloning sites will be carried along intact even if the fragment was inserted in the middle of the MCS.
• Plasmid data are saved under the plasmid's name overwriting previous versions. If you want to save the original plasmid, change the name before saving.
• You can enter a feature (e.g. a gene, promoter, etc.) by its start position and length (default) or by start position and end position. If the latter, "clockwise/counterclockwise" is chosen based on the end position.
• Each section (Plasmid Info, Features, Multiple cloning sites, Restriction sites) needs to be entered independently. You can't fill in multiple sections and submit them all at once.
• Multiple cloning sites - the text can be entered in any format. There's nothing special about the sample text, it's just a placeholder and example. (It's the way MacPlasmap showed MCS sites, so I'm used to it.)
• Restriction sites (or whatever else you want in these tags) can be added one by one, or in a batch. Batch format: One per line: "enzyme,position" (no quotes,no spaces)
• Restriction sites: You can opt to show (default) or not show the position in the map: e.g. "EcoRI (1234)" or "EcoRI".
• Once data have been entered they're displayed in the right panel. You can't edit them directly, although they can be deleted (check the checkbox beside the offending line, and click the "Remove checked" button at the bottom). You can then enter correct data as usual.
• Given a set of data, you can insert new DNA or cut out stretches. The "Insert/delete" button on the bottom of the right panel will give you the options.
• You can draw the plasmid (SVG format) at any point to see how it looks. The browser's "Back" button should take you to the data page again to make changes if necessary; or you can "Load saved plasmid" to revert to your saved version at any point.
• The plasmid can be drawn in SVG format only (default), in Postscript format only, or in both formats. If you select the "Postscript" checkbox you'll be given a link to download the .ps file.

Known issues

• Not much in the way of warnings or error handling.
• "Delete checked" has problems dealing with multiple items from multiple categories
• No locking on the tempfile (multiple simultaneous use will be a problem)
• Still problems with some tag text overlapping. Much improved; still occasional problems when enzyme sites are very densely clustered.
• Very long MCS are not displayed correctly, need to flip orientation Fixed?
• Postscript, SVG: text doesn't fit on very short genes.Much improved; only overlaps when two very small features are side by side
• "End position" vs. "Gene length" isn't working yet. Fixed?
• Postscript: Very short genes want to loop around twice ... Fixed?
• Arrow appearance isn't consistent with different plasmid sizes. Fixed?
• Some (unusual?) combinations of orientation, plasmid size, and gene length screw up positioning of gene and/or text. Fixed?