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!

MacVector 13 is almost out…..!

The next version of MacVector is almost ready to be released. MacVector 13 is more powerful and intuitive than ever. There’s not only some very useful new tools and features but MacVector 13 has had a redesign.

A fresh new interface

MacVector 13 looks great. The interface is now muted to suit the look and feel of Mavericks and many windows and dialogs have been rewritten and redesigned to be easier to use.

PBR322 Map and pBR322 Editor 2

Introducing restriction sites into primers with Quicktest Primer v2!

Adding restriction sites to your PCR products is now easy in the usual MacVector way. The Quicktest Primer tool first introduced with MacVector 12.6 has been enhanced to display restriction enzyme sites around the primary binding site of the primer.

Sites that are created or destroyed by mismatches in the primer or due to the addition of a tail are shown above the sequence. ‘One out’ sites can also be displayed below the sequence, color coded to indicate their potential effect on overlapping coding regions. The display is interactive so that when you “mouse over” a site, additional information is displayed. Clicking and holding on a “one out” site temporarily changes the primer and updates the entire dialog to reflect that change. Finally, double-clicking on a “one out” site makes a permanent change to the primer sequence.

QuickTestAnimation2

  • Existing sites in the template sequence are shown below the sequence in black.
  • New sites that will be introduced by mismatches in the primer are shown above the sequence in black.
  • Existing sites that will be destroyed by mismatches in the primer are shown in grey.
  • Putative “one out” sites are labelled with an asterisk as already used by the main restriction enzyme analysis tools.
  • Putative “one out” sites that are translationally silent are shown in green.
  • Putative “one out” sites that will change the amino acid sequence of the coding region are shown in red

NewImage

As well as displaying these sites the new tool makes it very easy to introduce the nucleotide change needed for the new restriction site into your primer.

  • If you mouse over one of the putative sites then the mismatched residue is shown in lower case and the recognition sequence of the site is displayed as a tooltip, aligned to the primer (as in the animation above).
  • If you click on a one-out site where the mismatched residue lies within the primer and hold the button down, the primer sequence temporarily changes, replacing the mismatched residue and showing any amino acid and restriction site changes above the primer.
  • Finally if you double-click the site it will make this change permanent in your primer.

Here’s some of the other new features in MacVector 13:

De novo NGS assembly

Velvet has been added to Assembler for enhanced de novo assembly of very short reads. Velvet is ideal for assembling Illumina sequencing reads of bacterial genomes on a mid range Mac. With paired read data it produces very good contigs. Now with Assembler you have many options for mapping and processing all your sequencing reads!

Redesigned results windows

All of the old style results windows have been rewritten and redesigned for easier visualization of an analysis and with a modern OS X appearance. All results for each sequence window are tabbed to stop window clutter. You can easily keep many results windows open for many different sequences at the same time.

PBR322 Results

Improved Applescript support

Applescript functions now allow control of file opening and saving. For example you will be able to script MacVector to batch open and save many files in a new format.

Testing Primers

A new mode has been added to the Design Primer tool for quick testing of pairs of primers.

Export trace file quality values:

A new tab in the Chromatogram sequence window displays the quality values and areas under each trace curve for each sequence residue in a tab delimited format that can be copied into Excel for additional analysis.

MacVector and Mavericks

MacVector 13 is fully compatible with OS X Mavericks. As well as Mountain Lion, Lion and Snow Leopard.

MacVector 13 is undergoing final testing before being released very soon.

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