University of Helsinki

Version 1.4.2: February 4th, 2008

• Improved "Align" Window. The alignment is now shown with line breaks, and it is possible to chose whether the show the Open Reading Frames or not. Also, a new "export to JPEG" allows to save the alignment image and print it using an image editing program.

Version 1.4: January 9th, 2008

• Reworked restriction enzymes strategy: PlasmaDNA now uses a standard database containing all the commercially available restriction enzymes, as maintained by REBase (http://rebase.neb.com/rebase/rebase.html). The database used is format number 32, gtype2c.XXX, whose current version is included in the PlasmaDNA package. Monthly upgrades can be obtained from this site. Since this corresponds to many enzymes, it is possible to select a subset of enzymes, eg those present in the laboratory, which is saved in the old Enzymes.pdat file. All the analyses can be made with either the whole or the limited set, using a button on the main window.
• The program can now analyze enzymes with degenerate recognition sites (ex AhdI, RsrII), or enzymes that cut outside of their recognition sequence (ex. SapI, BspMI). When using these enzymes to digest fragments, the proper overhangs are generated
• The Enzymes selection window now shows the restriction site and availability of each enzyme when the mouse passes over the name. For the availability, see the legend using the "availability legend" button.
• NEW WINDOW: Automatic Cloning. It is now possible to ask the program to suggest restriction sites for cloning experiments. Selecting the fragments containing the insert and the vector, as well as the parts of each that need to be found in the final contruct, the program suggests a maximum of 10 strategies, showing the enzymes used, as well as the digestion and ligation fragments that would be generated.
• PlasmaDMan has been modified to no longer allow modification of the restriction enzymes database.
• Improved ORF finding algorithm.
• Fixed a mistake made by the “Klenow” blunting routine.

Version 1.3.9: November 29th, 2007

• Improved ORF analysis: It is now possible to change both the genetic code used and the minimum number of amino acids found in the ORF for it to be considered (the old default was 150). The selection can be made from the ORF window of any fragment. Note that the changes will apply to all fragments, and come back to default each time the program is loaded.
• dam/dcm methylation: It is now possible to select the dam/dcm phosphorylation state of the template DNA when simulating a digestion. Enzymes with sensitivity to phosphorylated sites will behave accordingly. The choice is made when selecting the enzymes for a digest. On the drawing of the restriction analysis, the sites affected are denoted by an asterisk (*) after the enzyme name.
• To facilitate the design of a cloning strategy, enzymes generating blunt ends are now identified with a ¤ preceding their name on the drawing of the restriction analysis.

Version 1 .3.8: October 25th, 2007

• Align Window: this new window shows the various elements (open reading frames, domains, primers and restriction sites) aligned to each other and to the primary DNA sequence of the fragment. This window can be accessed from a new button in each fragment's menu. Feedback and suggestions for this new feature are welcome.
• Fixed ORF analysis bugs, specially for ORFs crossing the 0 position in circular fragments
• Fixed main window resizing bugs when deleting fragments
• Addition of a "Loading" window when the program loads. This describes what database the program is currently loading and helps identify problems if the program feezes.
• Other minor bug fixes.

Version 1.3.7: September 25th, 2007

• Added the possibility to attach comments to a project. Open the "Comments" window through a new interface button, and add the desired text. This text is saved with the project, and re-loaded when the save file is opened.
• Added a "BLAST" button next to every ORF in the ORF window. This will open the BLAST webpage (from NCBI) in the default internet browser, filling all the necessary fields. All that is left to do is to initiate the search using the "BLAST" button from the web page.
• Minor change: When opening a PlasmaDNA savefile, the first fragment is previewed by default.

Version 1.3.6: August 28th, 2007

• Fixed program freeze when clicking on the "Digest" button.
• Better visualization of the overhangs on the fragment graphic display
• New button: "Clear All", to start a new session without quitting and rebooting the program.

Version 1.3.5: July 11th, 2007

• NEW APPLICATION- PlasmaDNA Data Manager (version 1.0). Allows manipulations of the different databases used by the program. It is now possible to e.g. add new restriction enzymes, modify or delete primers, view or edit the sequences of the different domains in the databases without editing the database files with a text editor.
• Improved Enzyme selection window: it is possible to select enzymes cutting between x and y times.
• Better domain database management preventing the presence and drawing of duplicated domains, for example when the same domain is found in the local and the central database.
• Updated manual to include the PlasmaDNA Database Manager.

Version 1.3.2: June 26th, 2007

• Welcome window moved, the program now starts directly
• It is now possible to set up the 3' and 5' overhangs when entering a new fragment
• Improved ligation algorithm to prevent showing the same plasmid twice
• New "select subsequence" fields in the fragment info window
• New loading scheme: the fragments found in a save file or a FASTA file can be previewed to select the one(s) to add to the project
• ORF corresponding to coding sequences found in the database are now identified by name rather than number
• Look of the main window buttons changed
• Various changes for performance improvement
• Updated manual

Version 1.3.1: June 18th, 2007

• Repaired "Mung Bean" and "Klenow" buttons in the "Edit Fragment" window
• Non-palindromic restriction enzymes are now accepted
• Possibility to "Add new domain" directly by sequence.
• Fixed freezing when modifying the primary DNA sequence from the "Edit Fragment" window.
• Changed primer database format to accomodate mutagenesis primers (in a planned, future upgrade)
  

Version 1.3: April 2nd, 2007

• Completely new interface for the virtual digestion, including a virtual gel.
• Repaired "Add" from the PCR window.

Version 1.2.2: March 22nd, 2007

• Fixed compilation mistake that caused version 1.2.1 (Apple only) to crash frequently
• Added feature: Capacity to overlay a %GC curve to the graphical view of the fragments 

Version 1.2.1: March 19th, 2007

• Fixed memory leaks - IMPORTANT UPDATE
• You can now double-click on a fragment image to "show only"
• When more than 5 fragments are in the project, the main window becomes scrollable instead of expanding in size
• Various small changes for performance improvement

Version 1.1: March 2nd, 2007

• Fragments are now shown to scale compared to each other
• Improved color scheme
• Improved ORF-finding algorithm
• Fixed bug were the first letter of the names read from a FASTA file was missing