Changes in version 0.3 (Jul 2, 2009)

New Functionality

  • Kamino now supports primers, a new form of annotation. Primers are shown in sequence and map views, and make simulating PCR and Mutagenesis far easier and faster. Simply enter a primer name and sequence and Kamino will show you where and how that primer hybridizes throughout your sequence. Like features, primers are propagated to products when performing PCR, Mutagenesis, sequence edits, and cloning.
  • Primers shown in a new Primers view in addition to Sequence and Map views.
  • Primer hybridization is adjustable via a hybridization parameters dialog. Default hybridization options can be configured from the Preferences dialog. In addition to supporting continuous and interrupted hybridization schemes, Kamino can also allow a single base mismatch within the 3′ hybridized portion of the primer if necessary.
  • The PCR dialog has been completely revamped and now includes an embedded copy of the template. You can now select the primers you wish to use within the embedded document and auto populate the primer controls. Both preexisting and custom primers can be be used. PCR now supposes complex interrupted hybridization schemes.
  • The Mutagenesis dialog has been completely revampted and now includes a preview of how the mutagenic primer hybridizes (and mutagenizes) the template. Both preexisting and custom primers can be be used. Mutagenesis can now also be performed using a PCR product instead of a standard or custom primer. When using this approach, PCR product features are propagated to the mutagenized product.
  • You can now view ORF’s alone within Sequence. This the new default viewing option when showing translations.
  • Primers used for PCR and Mutagenesis can be reviewed from History view. Simply click the “Primer” or “Primers” button to the right of the operation. The shown primer information can be saved or printed. If mutagenesis was performed using a PCR product as the mutagenizing primer, this ancester can be resurrected just the template.
  • When an ancestral Annealing is shown in History view, you now get an “Oligos…” button. Clicking this pulls up a text edit that shows the oligos used and allows for making selections and copying the content, saving to a text file, as well as printing.
  • Added a Keyboard Shortcuts dialog
  • It’s now possible to shift arbitrary and codon based selections by 3bp at a time within Sequence view using new Opt+Left/Right keyboard shortcuts. You can now also extend an arbitrary or codon based selection by 3bp at a time within Sequence view using new Opt+Shift+Left/Right
  • Added shortcuts for removing selected/all enzymes (Cmd+Delete and Cmd+Shift+Delete) from the chosen set while using the Choose Enzymes dialog.
  • Added a shortcut (Cmd+Shift+Delete) for removing all enzymes from the chosen set while using the Choose Enzymes dialog.
  • Kamino now remembers whether you last viewed Map or Sequence view, and defaults to that view the next time you open that document.

Enhancements

  • When pasting DNA into various widgets (e.g. the New DNA File dialog), if the clipboard contains non-DNA characters that are not letters (e.g. spaces, tabs, line breaks, other symbols), Kamino now automatically proceeds by stripping these characters out and not asking if you actually want to do so. If the clipboard appears to contain a RNA sequence (U’s instead of T’s are present), you now are presented with the option of either a) converting from RNA to DNA or b) stripping out the U’s. If the clipboard contains non DNA, non RNA letters (e.g. protein sequence), Kamino will alert you to this and give you the option of stripping this out or canceling the paste. The summary, you can now paste RNA sequences and automatically convert them to DNA sequences, copied DNA should never produce a warning message before proceeding with a paste.
  • Improved printing of sequence view rulers, and printed headers in general.
  • Enhanced scaling and centering of maps when printing map view.
  • In history view, node names and lengths are now always placed below the respective nodes.
  • When flipping before inserting a fragment, history view now lists the fragment endpoints in clockwise fashion. The descriptive text now details that a flip then took place.
  • Improved the number and spacing of tick marks in for linear and circular maps.
  • Kamino no longer offers to be the default application for .txt and .rtf files on Windows.
  • Adaptive font size and ellipses are now used to improved how plasmid names and lengths are displayed for circular maps.
  • Enhanced the appearance of feature pliancy brackets.
  • Previously when viewing a lot of restriction sites in a linear map the linear strand was excessively compressed horizontally. Kamino now compresses a bit if necessary, but never nearly as much. Similarly, for tiny sequences Kamino no longer expands linear maps horizontally as far as possible. As a result features, ORF’s, and tick marks and labels should be far more readable for linear maps.
  • Kamino now remembers up to 50 recent files. You’ll still be shown only up to 10 of them. What you’ll find is if you delete some of the most recent files, the recent file list is not suddenly or quite empty.
  • Various textual, alignment, painting, icon and tab order enhancements.
  • For enzymes that cut the top strand at the end of a sequence view line, we no longer show the site on both lines.
  • After performing mutagenesis, the mutagenized product is now opened by default to sequence view and scrolled to the site of mutagenesis.
  • In order to add a shortcut for adding primers it was necessary to adjust other keyboard shortcuts slightly. The relevant ones are: Cmd + R – Make Primer Cmd + T – Make Feature Cmd + Opt + R – Duplicate Primer Cmd + Opt + T – Duplicate Feature Cmd + > – Select Range
  • When using the “Show Selected Feature(s)” and “Show Selected Primer(s)” commands, if feature/primers are toggled off in sequence/map view, you are now presented with a little dialog letting you know this and asking if you wish to turn features/primers so you can actually see the features/primers you toggled on.
  • When inserting a fragment (or two) between the endpoints of a linear vector, history view now reports location of insertion as “Insert between DNA ends” instead of “Replace End (#) — Start (#)”
  • When right clicking on hidden features in features view, the context menu now gives you the option to show the feature, not hide it.
  • Enzymes view’s mini map now detects which feature segment is under the mouse. As a result you now get more informative tooltips (with segment specific information) as well as the ability to select individual segments by Opt+clicking.
  • Replaced the “Reverse Complement” checkbox with a push button in the PCR and Anneal Oligos dialogs.
  • The cut locations button has been renamed “locations” and is only disabled if both enzymes and primers are turned off.
  • Optimized the map view layout code. As a result opening documents and showing embedded embedded documents within dialogs should be much faster. Resizing map view should also be faster.
  • Enhanced printing of genetic codes and the enzymes database.
  • When making a “bad” selection in a cloning dialog (neither an enzyme site or fragment) we no longer clear the enzyme controls. Instead the site/fragment listbox selection is cleared.
  • Removed unnecessary tooltip for current construct in history view.
  • Removed completion from the Find dialog. It got in the way and would cause problems. You can still reuse old queries by pulling down the menu and choosing one by hand.
  • Improved the default size of cloning dialogs on very large (30″ monitors)
  • In order to improve legibility, right aligned enzyme names in map view now have the cut location noted on the left instead of the right.
  • Improved the annotation of feature run-on translations.
  • More prominent stop codons.
  • When selecting a unique cutter in enzymes view, the unique site is also selected.
  • When the “Create Feature Segment” command opens a dialog with multiple options, you can now double click the feature within which you want to create the segment.
  • It’s now possible to manipulate mixed codon-arbitrary selections using the keyboard in sequence view.
  • Forward reading frame orange arrows now displayed on the right instead of the left.
  • When switching to Notes view focus is now automatically transferred to the comments field.
  • History View is far more compact then it was previously.
  • Since the document selection is never visible within Notes view, you can no longer interact with it within Notes view. For example, Select Range, Invert Selection, Copy Translation, and Copy Bottom Strand are now disabled when using Notes view. Pasting an enzyme selection will no longer fire up the Insert Fragment dialog and clicking within empty portions of the view will not clear the document selection.
  • When opening short (<= 100bp) sequences for the first time, Kamino now defaults to Sequence view.
  • When using the Find dialog, Kamino no longer automatically switches to Sequence view if currently in Map or Enzymes views.
  • In the PCR and Mutagenesis dialogs, clicking to transfer focus to the primer sequence no longer auto selects the entire primer sequence. As a result it’s now easier to extend a primer seuqence by adding bases at the beginning, end, or within.

Bug Fixes

  • Fixed various bugs that sometimes prevented the “Clone”, “PCR”, and “Mutagnize” buttons in the various cloning, PCR, and Mutagenesis dialogs from turning blue and becoming the default action once a valid protocol has been established.
  • Fixed a bug that caused the enzyme count header to report a number two greater than the actual number of chosen enzymes.
  • Fixed a bug that caused ORF endpoints to be off just a tad when shown in map view.
  • Fixed a bug that caused an initial click to choose an enzyme in enzymes view to be ignored after switching to that view.
  • Fixed a bug that prevented the “Choose from…” checkbox from being unchecked when a smart enzyme selection is manually modified (e.g. by adding an additional enzyme to the chosen set).
  • Fixed a bug that caused restriction site positions to be reported incorrectly (off by one) when clicking a line that represents multiple close sites in enzymes view / lines mode.
  • Fixed a bug that prevented the “Choose Enzymes” from automatically refreshing the chosen set when the “Choose from…” checkbox is checked and the “Chosen from” set is changed.
  • Fixed a bug that sometimes prevented the proper reading frame from being used when making features from ORF’s.
  • Fixed a bug that caused no enzymes to be shown by default after performing primer based mutagenesis if the template has an unsaved set of enzymes chosen.
  • Fixed a bug that caused the hand mouse pointer to persist after switching away from History view using keyboard shortcuts.
  • Fixed a bug that prevented scrolling to the bottom of sequence view for linear sequences that count from a negative base.
  • Fixed a bug that caused a files modification date to be updated simply by opening a document and without actually changing anything to do with the file or how it is displayed.
  • Fixed a bug that prevented cleavage triangles from being shown when mousing over or selecting restriction sites that cut at the origin.
  • Fixed a bug that caused Kamino to crash when trying to display the Translation Options dialog for a linear sequence.
  • Fixed a bug that prevented performing arbitrary deletions by first selecting an ORF.
  • Fixed various bugs that caused problems with ORF’s when reducing the minimum ORF length to 1.
  • Fixed a bug that sometimes caused the product name to be disabled while using the “Anneal Oligos” dialog.
  • Fixed various bugs that effected detection and display of ORF’s that wrap around the origin.
  • Fixed a bug that prevented the first lines top strand from being shown for linear sequences with an 3′ upstream overhang and count from a negative base.
  • Previously if you changed the font size to something other than Normal, then generated a valid product in a cloning dialog, the product was shown at the normal font size. This also occured when swapping the direction of the insert. This bug is now fixed, the Product should now always use the same font size as the vector and any inserts.
  • Fixed a bug where in the cloning dialogs, you could trigger the “Browse…” action by simply tapping down while the template control had focus.
  • Fixed a bug where when using a cloning dialog, if the active element does not have a loaded source then using the Find menu action would cause the application to crash. In such situations we now also disable the Go To action, which didn’t previously crash the app but gave you a useless dialog.
  • Fixed a bug that caused the application to crash if you Cmd+clicked a feature segment if no selection was present.
  • Fixed a bug that caused features created while features were toggled off to now show up in sequence view when features were toggled back.
  • When using the insert dialog, if you specify a linear vector you get yellow message letting you know insertion can only occur between the linear endpoints. Now, when you bring the insert dialog up again in the future, that message correctly no longer shown.
  • Fixed a bug that prevented actually changing the default ORF’s shown for new files.
  • Fixed a bug where a very long named document in the recent or open docs list caused column width allocation to get all messed up in the PCR dialog.
  • Fixed a bug that allowed the “Create Feature Segment” menu action to not be properly disabled when using the cloning dialogs.
  • Fixed various bugs that prevents various windows and dialogs from being moved while a sheet was shown.
  • Fixed various bugs involved with using the “Create Feature Segment” command.
  • Fixed a bug that prevented the “Minimize” command from being reenabled after a window is shown again after it was minimized.
  • Fixed a slew of bugs that prevented using the Cmd+W or File→Close menu action to close a variety of dialogs.
  • Fixed a bug where the direction of insertion controls could get out of sync when using the Insert Fragment(s) dialog for a second time.
  • Fixed a bug that sometimes caused the “Product with flipped insert” checkbox to read “Product with unflipped insert” in the Insert Fragment(s) dialog.
  • Fixed a bug that prevented proper tick marks from being shown on ancestral nodes after performing arbitrary insertions, replacements, deletions, or mutagenesis.
  • Fixed a bug that prevented pliancy and clicking to resurrect ancestral nodes if the mouse was over the ancestral node name but left or right of the map itself.
  • Fixed a bug that sometimes prevented enzymes and features from being displayed in History view.

Leave a Reply