What's New in MacVector 18.6?

Overview

MacVector 18.6 contains a wide variety of new or enhanced functionality, adding features such as one-click optimization of CDS coding regions, automatic phrap sub-project assembly of ABI reads based on naming, direct support of .csv and .tsv text files for Primer Database searching, optional inclusion of graphical information in GenBank exported sequence files and numerous tweaks and improvments to many different workflows.

MacVector 18.6 is a Universal Binary, meaning that it runs natively on both Intel and Apple Silicon ("M1" or "M2") Macintosh computers. It requires a minimum of macOS 10.13 (macOS High Sierra).

Direct Codon Optimization of CDS Features

There is a new Analyze function that will directly optimize codon usage of CDS features. Simply select a CDS feature in the Map or Features tab of a nucleic acid sequence and choose Analyze | Optimize Codon Usage for CDS… The resulting dialog lets you choose the codon usage table (.bias file) to use, along with the genetic code and the optimization algorithm. A filter dialog after the algorithm runs lets you choose whether or not to apply the results to the original CDS, or to simply view the proposed changes

Automatic Assembly of Sub-Projects with Phrap

There is a new tab in the phrap parameters dialog that lets you have MacVector automatically break out the input reads into sub-projects to be assembled separately. A simple pattern-matching text box lets you define which characters in the input filenames should be treated as project names, and which should be treated as read names. After assembly, contigs can be exported (to a variety of file formats, including fasta/q) retaining the project name in the contig names. A great time saver if you do a lot of related small sequencing projects using a well-defined naming convention.

Heterozygote Analysis Enhancements

There is a new checkbox to suppress the default normalization that the heterozygote analysis algorithm uses to better identify potential heterozygotes. Sometimes, clear heterozygotes may be missed if the combined peaks are significantly lower than would be expected in that area of the chromatogram. However, turning off normalization can result in an increase in false positives.

When performing a heterozygote analysis on assembled reads (Align to Reference or Contig Assembly) the output now includes the location of the potential SNP in the consensus/reference sequence.

Direct Support for .tsv and .csv Primer Database Files

The Analyze | Primer Database Search function (and the associated Scan DNA -> Primers feature) can now use appropriately formatted text .tsv or .csv files such as those that might be exported from Microsoft Excel, without having to import them into MacVector and save in the MacVector .nsub format. The data should have 4 columns – <Selected>/<Name>/<Sequence>/<Comment> where <Selected> and <Comment> are optional. If the <Selected> column is present, the values can only be “0” (unselected) or “1” (selected). The sequence should conform to the standard IUPAC code and “tails” on primers should be indicated by lower case. The use of a header row is optional.

Custom Genbank Export

There is now an option to export sequences in a GenBank text format that includes the graphical feature appearance information that is normally only available in MacVector .nucl files. GenBank is a simple text format, so you can view the resulting files in a text editor and its easy to modify the graphical information in those files if you need to. You can then import back into MacVector with those graphical changes fully intact. This new “enhanced” GenBank format can completely substitute for a standard MacVector .nucl file if you or your institution really requires a plain text format for submission to a database or other text-based repository.

Miscellaneous Enhancements and Bug Fixes

There have been some fixes to the Protein Toolbox Analysis code to help prevent certain very rare crashes.

The MacVector-specific ‘frag’ features now include the name of the user who made the change.

There is a new MacVector-specific ‘edit’ feature that describes edits made to a sequence with the date the change was made and the user who made the change. Currently, this is only created by the Optimize Codon Usage for CDS function, but eventually this will be the basis for a comprehensive history function throughout MacVector.

The Restriction Enzyme Picker has been updated to display the number of cuts for each enzyme.

Invoking Select All in the Restriction Enzyme Picker now ONLY selects the VISIBLE enzymes in the picker. This makes it much easier to manipulate lists of interesting enzymes.

There is a new <ctrl>-click context sensitive menu item in the Contig Editor and Align to Reference Editor that lets you manually change the “clipping” (also known as “trimming”) positions at the beginning and ends of sequences.

There are enhancements in the Align to Reference scoring algorithm to more closely reflect parameters set by the user.

There is a “mouse-over” tooltip in the Align to Reference and Contig Editors that displays more information about the read and the alignment score.

The window size of each type of window is now remembered each time you close one, so that a subsequent window of the same type will open at that size.

There is now a <ctrl>-click context menu item to control how read names are truncated in the Align to Reference and Contig Editors.

You can now hold down <option><shift> to temporarily switch from the normal “Zoom To Sequence” mode in the Map tab to “Select Sequence”.

Phrap parameters are now remembered between invocations like most other MacVector parameters.

The licensing code has been cleaned up to do a better job or reporting when licenses are in use on the local network.