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Free, Publication Quality Plasmid Annotation

free-automatic-plasmid-annotationI just came across an extremely nice piece of plasmid mapping and annotation software that I’d like to share with you. PlasMapper is a web-based application, created by staff from the University of Alberta, that automatically generates fully annotated plasmid maps from your raw sequence input.

Using a database containing the sequences of hundreds of features (replication origins, antibiotic resistance cassettes etc), as well as restriction enzymes, the program identifies each of the features in your inputted plasmid and renders them in a publication quality graphical or text map. The image on the right shows some examples of the output of the application – click the image to view a larger version.

Users have options to add their own features to the plasmid (e.g. cloned-in genes or other features not in the database) as well as to change the color scheme, annotation features and restriction enzyme annotation. Another neat feature is a built in database of commercially available vectors, so you can be up-and-running immediately if you are using one of those. Excuse me for getting excited but this free program does a far better job at this particular task than a certain commercial vector handling packing my lab paid several thousand dollars for just a few years ago!

You can find PlasMapper here and the publication that describes the program here. The whole application can also be downloaded and run from your own lab server if you have one.


  1. max on December 4, 2008 at 4:17 pm
  2. max on December 4, 2008 at 4:16 pm

    Hi I am using the APE program. It’s free, small, doesn’t have a lot of functions, doesn’t require a registration, runs on all operating systems, but does has a strange user interface sometimes.

  3. Nick on November 21, 2007 at 3:07 pm

    Hi Regis. Thanks for your comment… I use a mac too – don’t get me started on windows! 🙂

  4. regis on November 21, 2007 at 2:58 pm

    Great application, I like that´s is web based also, so I don´t have trouble on my machines to run it (I have a Mac and yes, I can run windows, but its easier, and far cheaper, to run it w/o windows…)

    Great site, I´ve recommended to many lab colleagues, and all say “great! thanks”, please continue with your nice work.


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