What's New in MacVector 12.7?
MacVector 12.7 has a new Cloning Clipboard that dramatically simplifies the creation of new DNA constructs. The new functionality not only lets you join molecules together using an intuitive drag and drop interface, but also lets you easily accomplish cloning constructs that were difficult with earlier versions of MacVector.
There have been some significant performance enhancements to the Dot Plot (DNA Matrix) analyses and to the Align To Reference analyses, allowing you to now run pairwise alignments of whole genomes in just a few minutes or to align hundreds of thousands of NGS Reads against a reference genome in an hour or so. A full list of the changes can be found in the Release Notes.
There is a new window available called the Cloning Clipboard that maintains a history of the DNA fragments created each time you use the Digest function. For example, if you select two restriction enzymes in a Map tab, then click on the Digest button, the fragment between the sites gets placed on the Cloning Clipboard. You can then join fragments together directly on the Cloning Clipboard by clicking on one end of a fragment and dragging to a different end, as shown in the animation below;
You can also join incompatible ends by filling in or cutting back the overhangs and you can create a new sequence window in MacVector by selecting a fragment and clicking Circularize, or by simply double-clicking on a fragment. A selected fragment can also be directly pasted into an existing target vector by highlighting appropriate destination restriction enzyme site(s) and clicking Ligate.
Align To Reference Performance Enhancements
A number of operations in the Align To Reference functionality have been optimized to be of more use for aligning large numbers of Next Generation Sequencing reads against large genomes. Importing reads is now very much faster (in many cases 100x faster) and aligning reads is from 5x to 50x faster. With the appropriate parameters, you can now align several hundred thousand reads against a typical bacterial chromosome in just a few hours. Individual edits in the Editor tab with several hundred thousand reads are now effectively instantaneous (previously they could take many minutes while the consensus was recalculated). In addition the text in the SNP tab is generated anywhere from 10x to 1,000x faster than previously. Finally, although generation of the text in the Text tab has also been significantly speeded up (again up to 1,000x) it also now runs as a separate thread so you can cancel the operation if it takes too long. To align short reads against a genome, import the reads from a FastQ file using the Add Seqs button (at this stage, we recommend you keep the number of reads below 250,00), then try the following alignment parameters;
Under these conditions, 50 nt reads will align against a 7 Mb genome at the rate of about 1000 reads per minute on a slow laptop.
Optimized Reverse Translations
There are new options in the Analyze | Reverse Translation dialog, allowing you to optimize codon usage when reverse translating a protein. You can now request that the generated DNA sequence uses only the most popular codons from a given codon bias file, or that the generated sequence should have an overall codon usage that most closely matches the codon bias file.
This is the first release of MacVector that does not simply refuse to run when a temporary license (i.e. a trial license or an annual license) expires. Instead, it continues to work, but with reduced functionality. All of the functions in the Analyze menu become disabled but most other features still work as normal. This means you can still open, edit, save and print MacVector documents, or save MacVector files in other formats. You can perform simple click cloning operations (but not the new Cloning Clipboard), generate new constructs and have full control over the appearance of features. Entrez and BLAST are still available along with the Find functionality. This will let licensed users share MacVector files and data with more casual users without having to convert sequences into a common format, often losing information (such as graphical appearance and layout) in the process. For more information on MacVector Free, please visit this page.