Monday, May 3rd 2010

QuickGene Update 1.1 - Introducing Methylation Warnings

This latest update brings you two handy, new features and a plethora of changes and improvements. The smallest of the two features comes in the form of an unobtrusive, little lock in the corner of the sequence (1), which, with a simple click, helps protect your data from being modified while still providing all the useful information you need. No longer will and inadvertent bump on your keyboard knock everything in your file out of frame!

The second feature is the ability to receive full-fledged methylation warnings (2). When enabled, all visible restriction sites that are potentially blocked or inhibited by Dam or Dcm methylation are marked by a red dot. When hovering the cursor over it for extra information, not only is the usual tooltip with optimal reaction conditions and the recognition sequence displayed, but the exact location and sequence of the methylation site is also unveiled. Everyone accidentally forgets about methylation sooner or later, wasting time and costly enzymes and reagents. Now, you can forget about it and let QuickGene keep an eye out for you!

Of course, we've been listening to everyone's feedback and have made many more changes and repairs, such as the ability to save extra data in Fasta files, improved integration with Mac OS X and enhanced compatibility with 64-bit Windows systems. The enzyme manager has also been redesigned in anticipation of an exciting, upcoming feature. More on that next month!

New features

  • 1 Added methylation warnings. Cut sites that are influenced by methylations are now marked with a red dot.

  • 2 Added a button to lock the sequence, preventing accidental changes.

  • Integrated native Mac interface controls, namely:

    • When the loaded project has unsaved changes QuickGene will show a red marker in the Close button.

    • The search field now looks and feels like the common Mac search fields.

  • Added the ability to save sequence- and project-specific data such as descriptions and notes in Fasta and GenBank files.

  • Redesigned the enzyme list window and implemented the following changes:

    • Significant performance improvement.

    • More versatile copying and moving enzymes to other lists using the context menu.

    • Split enzyme table and info panel into two different views: either the table is visible, or the panel is visible (with enzymes shown in a single column list)

    • Copying enzymes from a list to another list by dragging from the grid to the name of the target list now also works on Mac.


  • Simplified the problem reporting dialog and added the possibility to attach files.

  • Improved loading and navigation speed on the statistics tab.

  • Improved compatibility on 64-bit Windows systems.

  • Updated the Help content.

Solved problems

  • Recognition sites weren't properly displayed across the first and last base pairs in circular sequences.

  • When copying and pasting the reverse strand or the reverse complement, the features were positioned incorrectly and would point in the wrong direction.

  • Active search results could be edited, causing various problems.

  • Active search results weren't updated when the sequence was edited.

  • The updater could, in some cases, require administrator privileges under Windows Vista/7 and QuickGene would fail to prompt for UAC.

  • RNA sequences would display the complement as a DNA strand.

  • Using an & character in the description or name of a sequence or project could corrupt the project file.

  • Maps saved as image files would show rough edges that were not visible in the map view itself.

  • QuickGene could fail to start in rare cases when JVM and SWT library platforms did not match.