Tuesday, February 2, 2016

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)*

Using the map of pX330 below

The original "Complete Sequence" window
 The new "Complete Sequence" window



pLOT 1.0.10e Download Links
pLOT v1.0.10f Patch (Requires full installation of 1.0.9f or 1.0.10e)
pLOT v1.0.10f patch 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.

Monday, February 1, 2016

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.

Wednesday, December 16, 2015

pLOT 1.0.10d

  The 1.0.10d patch fixes a bug that sometimes causes pLOT to abort saving the file.  It also fixes a bug in the restriction digest enzyme mixes.


pLOT 1.0.10d Download Links
This requires the full installation of 1.0.9f.

pLOT v1.0.10d Patch [Link 1]

(if you get errors about the version of the pLOT.dll, use this link instead)
pLOT v1.0.10d + pLOT.dll [Link 1]

  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.

Friday, December 11, 2015

pLOT 1.0.10c

  The 1.0.10c patch fixes some bugs with the resizing of zoomed in maps and the drawing of arrows in when the map is zoomed in.  It also allows the fonts on one side of a circular map to be larger than those on the other side if the other side's font size has been reduced due to the number of labels on the screen.


pLOT 1.0.10c Download Links
This requires the full installation of 1.0.9f.

pLOT v1.0.10c Patch [Link 1]

  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.

Thursday, December 3, 2015

pLOT Version 1.0.10ab

  pLOT v1.0.10b is now up.  In addition to a few possible bug fixes, you can now specify enzymes by the number of cuts and position in the sequence.  An updated Restriction enzyme file has also been included that removes a couple double entries.  Note that currently, the filtered enzyme selection does not save to the save file.  This will be added shortly.  Filters do not take into account the blunt/staggered cut, etc... parameters.

Sunday, November 29, 2015

Version 1.0.10a will hopefully be out this coming week (probably later in the week rather than sooner).  This update will allow the user to show enzymes based on the number of cuts found in a given region.  For example, enzymes that cut only once in the first 3000bp of a vector but 0 times in the remaining, etc...  More than one selection criterion may be used.  Below is a screenshot of the current test version.

Before Selection

Selection Window


After Selection


Friday, September 25, 2015

Update 1.0.9K

pLOT update 1.0.9k 

   pLOT update 1.0.9k is now up.  The tools menu now has an option to scan the sequence for upper and lower case stretches and annotate the uppercase as exons (naming them starting at "Exon 1" and going to whatever is last).  This is useful if you are importing sequences from the UCSC genome browser that have many exons and you don't feel like annotating them individually.

  In the UCSC Genome Browser, select the genomic region for your gene of interest and make sure the options for exons in uppercase is selected.  Click the submit button to retrieve the sequence.
 

Copy the sequence (not the header) 


and paste into a new pLOT project and click OK.

Once the sequence is loaded, select Tools > Convert Uppercase to Exons

And voila!



pLOT 1.0.9k Download Links
This requires the full installation of 1.0.9f.

pLOT v1.0.9k Patch [Link 1]

  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 or email me explaining the error so that I can implement a fix ASAP.