PLOT Plasmid Mapper

23/02/2026

A new update is now available. A few GUI/bug fixes implemented as well as an updated version of the Gibson Designer plugin. The update can be downloaded from the blog or directly from the link below.

Update: pLOT-J 2026-02-23 January 4, 2019 admin Leave a comment The new update to pLOT introduces Plugins capabilities. Plugins are simply Java (.jar) files that can be used to automate… Continue Reading

08/12/2025

I'm in the last stages of a new update for pLOT. In addition to general but fixed, etc... the new version will be able to switch themes without needing to restart.

05/11/2025

An update was posted today that restored the primer categories in the the show/hide primers button's dropdown menu. This feature went missing due to some changes in the menu handling and is now fixed. Apologies for the bug.

08/10/2025

The newest update of pLOT is available for download (link below). This update fixes some issues and adds quality of life updates such as filtering primer categories in the primer selection menu on the main screen (by right clicking the toggle primers button). It also add Plugin functionality. Included are a few plugins I made for my own use, including a Gibson primer designer. Plugins can be accessed from the PlugIns menu of the main screen's menu bar.
A plugins template source is included in the zip file (made using Netbeans). Additionally, by request, the antisense translations of selected features can now be seen in the lower Feature Viewer as well as in the Sequence Editor window. The reading frames can be toggled on and off from the view menu like the normal sense reading frames. Additional plugins will be available if I make some that seem like they would be useful.

Blog link:

Update: pLOT-J 2025-10-08 January 4, 2019 admin Leave a comment The new update to pLOT introduces Plugins capabilities. Plugins are simply Java (.jar) files that can be used to automate or manipulate the sequences in the pLOT window, make their own windows, or any number of other things. Plugins sto...

22/09/2025

The new version of pLOT is almost ready. This includes updates such as the use of user-made plugins and the ability to toggle the antisense reading frame translations in the sequence viewer below the map and when editing the sequence in the Sequence Editor window. Some example plugins will be available for download including source codes including a Gibson primer generator that generates primers (obviously) for Gibson assembly in a table and optionally as the final expected sequence map with fragments assembled, primers, PCR products, and non-template sequences (if any) annotated.

03/07/2025

Coming soon, an update for pLOT allowing for the use of custom plugins (if you write Java). This will implement two types of plugins. The first is custom file decoders and encoders that allow you to read or write custom/otherwise unsupported formats, and the second is Tools plugins that allow you to write and use custom sequence manipulation or various other types of tools.

11/02/2025

An update has been posted that fixed an error that could occur when reverse complementing a sequence. The primer editor window is also updated away from the table view as this made editing comments more difficult.

27/09/2024

The newest update to pLOT-J has been posted. This patch fixes a number of previously unidentified bugs and adds features. To see changes, click the "About>Show Help" menu item from the main window and click the "Updates to this version" link at the bottom of the page.

22/08/2024

A new update will be posted in the next few days. The change log for versions will be accessible through the main window's About > Show Help menu. This will open the help window which has a link at the bottom of the page for the changes, known bugs, and bug fixes section. This version fixes a number of bugs including the search window's lack of finding all instances of sequences with gap characters.