Version 0.4.4

By December 14, 2010Release Notes From Blog

Changes in version 0.4.4 (Dec 14, 2010)

New Functionality

  • Kamino now opens Vector NTI DNA files, both individual files (.gb extension) and archives (.ma4 extension). Feature annotations are preserved.
  • You can now ligate two or three fragments to make a linear ligation product.
  • As long promised, Kamino provides versatile controls for editing the ends of linear DNA sequences.
  • You can simulate a partial fill-in of a 5’ overhang.
  • Added mouse wheel gestures for zooming (Ctrl + scroll vertically) and sliding the zoomed region (Ctrl + scroll horizontally).
  • Added a keyboard shortcut (Ctrl+L) for simulating Agarose Gels.

Enhancements

  • Key information about unusual enzyme properties is provided in tooltips and in the Restriction Enzymes window. Also add Eco53KI to the enzyme database.
  • When switching between documents or chosing the generic genetic code used to display ORF’s in a dialog with multiple documents (e.g. cloning dialogs), the Genetic Codes dialog now auto refreshes to show the relevant genetic code for the visible document.
  • Various textual, color, icon and default focus enhancements.
  • The application name and version number in the launch dialog is now a link to the releases page.
  • When viewing a sequences history, to the right of isolate operations we now provide a “Details” button if either end of the isolated fragment (a cloning intermediate) was modified by blunting or partially filling in before being ligated to form the product. History colors are now also provide for such operations.
  • The copy tool bar button is now enabled and allows you to copy the bottom strand in the 5′ to 3′ direction if only bottom strand bases are selected.
  • Sequence view now scrolls horizontally if necessary to show a newly selected range.
  • On Windows you can now quit Kamino by clicking the X button in the launch dialog or tapping escape.

Bug Fixes

  • Fixed a bug that prevented Kamino from running on Windows XP
  • Fixed glitches with exporting linear maps to rasterized formats (e.g. PNG)
  • Fixed a bug that prevented shift-selections of arbitrary ranges when using the Destroy Restriction Site dialog.
  • Fixed an obscure crash bug in the DNA sequence compressor for sequences shorter than 18bp. This could come into play when using the Anneal Oligo dialog.
  • Fixed a potential bug with inserting fragments near the end of from large sequences into smaller vectors.
  • No longer exporting the documents code number using the GenBank DEFINITION field.
  • Fixed a bug where if you changed the zoom window while using Enzymes View’s Numbers mode, when switching to lines mode the actual set of visible features were not shown until you adjusted the zoom window again.
  • Fixed a bug where if you deleted or renamed a recent file while Kamino was running, then tried to load that file in a dialog, Kamino would crash.
  • When loading an empty document (e.g. when resetting the product tab in a cloning dialog or resetting a vector/insert/fragment tab when the modified open document is closed without saving changes) we now clear the chosen enzyme set combo box in the Enzymes view.
  • Fixed a bug where if sequence endpoints were used in subsequent steps they would be displayed twice in history view.
  • Fixed numerous stability bugs.
  • Fixed a bug where if only a portion of the top strand is selected the “Copy Bottom Strand” menu should be disabled.
  • Fixed a bug where if you selected an entire sticky overhang the selection color extended down (or up) to the horziontal ruler line in sequence view when it really should only encompass that strand. We only extend the selection down to the central ruler line if bases in both strands are selected.
  • Fixed a bug that prevented the I-beam cursor from being shown while the user has pressed and held the mouse button when doing a shift selected.
  • Fixed a bug where when painting history colors for linear maps the color for the right most range did not run to the end of the sequence when it should have (one black column of pixels remained at the right).
  • Fixed a bug where if you deleted part of a linear sequence near one of the endpoints the red-black and blue-black gradients, shown when history colors are enabled, would erroneously wrap around the origin even though the sequence is linear.
  • Fixed a bug where software update could fail on Mac OS X when run from a non Administrator account.
  • Fixed a bug where selections within sticky ends were often displayed incorrectly in map view.
  • Fixed a bug where when using the “Cut” command the length was sometimes reported incorrectly (say when cutting entirely within an overhang).
  • Fixed a bug where unsaved sequence case changes were not shown in cloning overviews.
  • When generating isolated fragments for say the “Cut Vector”, “Cut Insert”, or “Cut Fragment”, if either end is blunted we now longer show the enzyme name in <‘s in the product since that end has been modified.
  • Fixed a bug where if you placed the cursor at the end of a sequence, then tapped Cmd+Shift+Left, Kamino would not select the DNA you would expect.
  • Fixed Fermentas enzyme links.
  • Fixed the bottom cleavage location for BspQI.
  • Fixed bugs with modifying features when using the PCR dialog.

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