General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

What’s New in MacVector 11.1?

As mentioned in the last few posts MacVector 11.1 is a release designed to consolidate and ‘tweak’ the many new features and changes that have been made over the last three years. In the main these changes are designed to simplify and speed up many common workflows as well as providing better integration with OS X and improving performance. However, there’s also some longstanding bugs that have been fixed and as usual a great deal of these changes have been made in direct response to users’ feedback. On that last point, as ever we encourage you to let us know what you think about MacVector, and whereas we always welcome emails to “support@macvector.com” and phone calls, we will be running a survey towards the end of this month to elicit feedback. The last survey we ran was quite a while ago now, and we got a some extremely valuable feedback. Incidentally we offered one of the new video iPods for one lucky winner last time, what cool new device from Apple could we offer this time…..!

We’ve mentioned a few of these changes over the last few posts, here’s an overview of the notable ones.

General

– Many of the analysis functions now use drop down window-modal sheets rather than application modal dialogs, allowing you to continue to work with other windows to prepare, view or copy data required for the analysis. Many of the sheets have a convenient new history combo box that keeps track of the various data files or target folders used in the dialog to allow rapid switching between commonly used files.

– Multiple levels of Undo have been added to the Trace, Multiple Sequence Alignment and Contig/Align to Reference editors. All three have also had extensive work to streamline workflows, add keyboard navigation and fix various display glitches and crash bugs.

– Dialogs to locate auxiliary data files (Restriction Enzymes, Matrices, Codon Bias tables etc) now all default to the appropriate location in the MacVector distribution folder.

– Align to Folder, Restriction Enzyme, Proteolytic Enzyme, Nucleic Acid Subsequence, Protein Subsequence, Translation and Reverse Translation are now all window modal dialog sheets.

– You can now drag a selection from one sequence window and drop it into another single sequence window or into an external application (e.g. TextEdit or Microsoft Word) that can accept drag and drop text.You can also drag selected text out of a result window and drop it into other acceptor windows e.g. Microsoft Word or Text Edit (OS X 10.5 and above only).

Subcloning

– You can now select any graphical object (e.g. a feature) and Edit | Copy will copy a blunt ended copy of the underlying sequence to the clipboard.

– The Ligation dialog now treats sequences copied from external sources or the sequence editor as blunt-ended fragments.

– Restriction/Proteolytic Enzyme – you can now specify the minimum number of cuts as well as the maximum number of cuts when filtering (or setting up) the results. The selected enzyme data file is now displayed in a history control so you can quickly swap between commonly used files.

Sequence Analysis

Protein Analysis Toolbox – the AA Composition, pI and MW protocol now also displays the predicted extinction coefficients and aliphatic index. In addition, the pI and molecular weight calculations have been revised for increased accuracy.

– NA/AA Subsequence – the graphical Map result window is now linked back to the parent sequence so that selections in the result window are propagated to the parent editor.

– The Subsequence editor has been reworked as a dropdown dialog sheet and you can now copy/paste into the Sequence edit box. These changes let you easily paste primers from external applications or from other MacVector windows into a subsequence file to maintain a database of useful primers.

– There is a new “Show Dots” button that can optionally be added to the MSA editor toolbar (right-click on the toolbar and choose Customize Toolbar… to add the button). This represents matching residues in an alignment with dots rather than the residue itself.

Growl installed on your machine, the Job Manager will use Growl notifications when a job has completed rather than bounce the icon in the dock.

– There are now keyboard shortcuts to switch between tabs – hold down the apple command key and type “1” to switch to the first tab, “2” for the second tab etc.

– “Dirty” windows now display a dot in the red window close button.

– Text windows and tabs now support standard keyboard and mouse selections.

The above list hardly scratches the surface of the full list of changes. You can check out the full list in the release notes.

MacVector 11.1 will be released in a few days.

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