**** UPDATE ****

As of 12-01-2016, the pLOT blog has moved to its own website.  This means no more externally hosted files with ads, etc...

Stop by the new blog at

www.PlasmidPlotter.com!

pLOT 1.0.12c is now up.  This update fixes a few bugs that had previously been overlooked.  pLOT 1.0.12c requires the full installation of 1.0.12a.  If you have not installed 1.0.12a previously, uninstall your current version and run the 1.0.12c full installation setup.  If you have already installed 1.0.12a, simply copy and paste the patch file to your pLOT directory.

 pLOT 1.0.12a is now up.  This update requires uninstalling any old version and performing a complete installation of the update.  This version changes a number of things.

  pLOT 1.0.11h update is now available.  This update causes restriction enzyme cut sites to be highlighted when the mouse hovers over it.  If more than one site is present for a given enzyme, all of the sites highlight in response, allowing the user to easily locate them.  The forecolor (text color) and backcolor (highlight color) can be customized in the Preferences window under the Restriction Enzyme tab.

Map when mouse is not hovering over the ApaI.

Map when mouse is hovering over the ApaI.

Preferences window with highlighting options.

  The pLOT 1.0.11g fixes a few bugs including one where changing the sequence in sequence editing window did not always result in updating of the restriction sites, primer locations, etc...

  This pLOT update fixes a few bugs in the program and now displays the scoring of individual parts of promoter elements found during searches.  The -35, -10 box scores and spacer length, %GC and score are displayed.

  This pLOT update fixes a few bugs in the program including a bug that mis-colors single base pair annotations in the Edit Sequence window.  The version says it's "d" instead of "e" in the "About" menu but this is the "e" release.

    pLOT update 1.0.11d adds the ability to custom-color labels for annotations.  If no color is specified, the default color set in the Preferences window is used.  The color can be changed either by

  pLOT 1.0.11c allows for pattern searching for prokaryotic promoter-like sequences as well as Shine-Dalgarno- and Kozak-like sequences.  The searched sequences can be added as features from the window and their associated ORFs can be optionally annotated as well.

  pLOT 1.0.11.5c adds a fix to the virtual gel that could cause the program to crash under certain circumstances.

pLOT 1.0.11.5c Download Links

pLOT v1.0.11.5c patch file [Link]

If this is the first time you're installing pLOT, use 
this first 1.0.10j full installation [Link]

  Like the pLOT Facebook Page for up-to-date information on new releases, previews of upcoming release features, to report bugs, to suggest new features, or to volunteer as a beta tester.  You can also subscribe to follow this blog for email notification of new posts.  If you experience any bugs or glitches, please feel free to leave a comment, Facebook message, or email me explaining the error so that I can implement a fix ASAP.

  pLOT 1.0.11b adds a few more fixes as well as a early stage bacterial promoter search tool.  The tool can be found under the Tools menu.  Clicking on an annotated feature prior to opening the tool window will set the search region to the region of the annotated sequence.  You can change it manually in the window.

  pLOT 1.0.11a adds a few fixes as well as the ability to uppercase, lowercase and antisense selected sequence from the View/Edit sequence window when you right click the mouse.

   pLOT 1.0.10j fixes a bug in the View/Edit Sequence window where typing in a base entered only the uppercase even if the lowercase was entered.

   pLOT 1.0.10i fixes a bug in the View/Edit Sequence window that can shift feature annotations when the Ctrl+C key combination is used to copy a highlighted text.  Additionally, a menu is available in the same window on right click when sequence has been selected that allows for copying of the sequence to the clipboard in a variety of formats.

   pLOT 1.0.10h is a minor patch that fixes the Edit Annotations (Ctrl+E) so that when you open it, it automatically goes to the feature you last clicked.  This was functional in the pre-1.0.10g version and got inadvertantly removed when changes were made to some code to accommodate the View/Edit sequence window.  A few other bugs have been fixed as well as the Tab order in the Annotations window.

pLOT 1.0.10g is out.  This update introduces the ability to edit the sequence and feature annotations from the "View/Edit Sequence" item under the "Edit" menu.  Aside from editing the sequence itself, you can now change.

* Edit: The link to the 1.0.10e full installation is fixed.  It was previously the link to the patch only *

The Edit Sequence Menu

A right click on a selection gives the option to edit any of the features selected.  Moving the cursor with the direction keys or mouse results in the lower status bar displaying which feature(s) you're on.

pLOT 1.0.10F

pLOT 1.0.10f patch (If you have previously run the 1.0.9f or 1.0.10e full installation) is now up.  A bug in the that sometimes caused the program to crash at startup if the last instance was closed at a certain height has been fixed.  Additionally, the View\Complete Sequence menu now opens the complete sequence in a new window that has the base pairs colored by their features' colors.  Moving features forward or backwards in the drawing order affects which color is shown between overlapping features.  Moving the cursor in the window or highlighting text causes the status bar at the bottom of the window to tell you which feature you're on/have selected.  This is a transition step to having the ability to edit the sequence in this window which has not yet been implemented.  See images below.  A few bugs that crept in during the addition of the undo/redo code has been fixed.

*Edit The View\Complete Sequence menu has been moved to Edit\Edit Sequence (Ctrl + Q)*

pLOT 1.0.10e patch (If you have previously run the 1.0.9f full installation) and full install (for new installations) are now up.  This update now has added an undo and redo button on the main window.  Alterations to the sequence, feature annotations, restriction enzyme selection, etc... can be undone or redone.  A bug in the restriction enzyme window that made it search for the sites unnecessarily has been fixed.

pLOT 1.0.10e Download Links

pLOT v1.0.10e Patch (Requires full installation of 1.0.9f) [Link 1]

pLOT v1.0.10e Full installation file [Link]

  Like the pLOT Facebook Page for up-to-date information on new releases, previews of upcoming release features, to report bugs, to suggest new features, or to volunteer as a beta tester.  You can also subscribe to follow this blog for email notification of new posts.  If you experience any bugs or glitches, please feel free to leave a comment, Facebook message, or email me explaining the error so that I can implement a fix ASAP.