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.

Thursday, June 11, 2015

pLOT update 1.0.9j

pLOT update 1.0.9j 

   pLOT update 1.0.9j is now up.  A bug in the reverse/complement code that did not update the restriction enzymes has been fixed.  A bug in the Features Library export has also been fixed.  A bug that sometimes made a line in arrows extend too far has been fixed.


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

pLOT v1.0.9j 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.

Thursday, April 9, 2015

pLOT update 1.0.9i 

   pLOT update 1.0.9i is now up.  It now imports sequences directly from the *.Ab1 chromatogram files.  A note is that I have access to chromatograms from only a limited number of different machines (due to out sequencing core) so this may not open some files generated by older machines.  I haven't encountered such problems yet but that's no guarantee.


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

pLOT v1.0.9i 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.

Wednesday, March 11, 2015

  Well I'm finally moved in, have internet restored and getting along at the new job so here is an updated patch that fixes a problem with the names of restriction enzymes on the virtual gels  Sometimes the names came up as all "AarI".  That should be fixed now.  Other fixes and additions will be coming shortly although I'm pretty busy so they will be a bit slower than before.  Coming up in the next full release will be the ability to open Ab1 sequencing files as well as some fixes.  Among oher file formats I plan to allow to import from in future releases will be *.SCF chromatogram files, SnapGene *.DNA.

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

pLOT v1.0.9h 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.

Friday, January 9, 2015



Minor patch to pLOT 1.0.9g.  The start and stop positions are now shown in the correct order when hovering over a feature, a minor fix to restriction site numbering in the RE window, and the Sense/Antisense selection button now correctly disappears when editing the comments in the Annotations window.  A bug that caused a crash when restriction enzymes that were not present in the sequence are specified in the file has been fixed.

pLot 1.0.9g Download Links
This requires the full installation of 1.0.9f.

pLOT v1.0.9g 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.

Sunday, January 4, 2015

pLOT 1.0.9f



pLOT 1.0.9f if now out with some fixes and updates.  Apologies for the length of time it took to release.  We've been moving and have had only sporadic internet and free time.