What's New in MacVector 18.7?

Overview

MacVector 18.7 contains a wide variety of new or enhanced functionality, adding features such as long-read genomic reference alignments using the popular minimap2 algorithm, batch translations of individual genomes and/or folders of sequences, visualisation and creation of codon usage tables from individual genomes or folders of sequences along with the usual set of bug fixes and workflow enhancements.

MacVector 18.7 is a Universal Binary, meaning that it runs natively on both Intel and Apple Silicon (M1/M2/M3/M4) Macintosh computers. It requires a minimum of macOS 10.13 (macOS High Sierra).

Long-Read NGS Reference Alignments using minimap2

If you have the Assembler module, you can now assemble noisy long-read data from Pacific Biosciences or Oxford Nanopore using the popular minimap2 algorithm. This is similar to bowtie but can handle long reads whereas bowtie is optimized for short (<500nt) reads. To use minimap2, create a new Assembly Project, then click on the Add Ref toolbar button to add one or more reference sequences. Then click on the Add Reads toolbar button and select one or more NGS data files. While not essential, it is usually also a good idea to double-click on the Status column of each read to let MacVector know exactly what type of data you are analyzing. Finally click on the Assemble toolbar button and select minimap2 from the menu. The simplest option is to choose one of the presets in the resulting dialog that will tune the assembly parameters for your specific type of data. Note that minimap2 is actually very good at assembling short read data and in some circumstances may out-perform bowtie.

Translate All CDS Features

There is a new Analyze | Translate All CDS Features… menu item that lets you batch translate all CDS features in the active sequence. You might typically use this with an entire annotated bacterial genome, though it works just as well with eukaryotic sequences. There are options to display (and then copy or save) all of the translated proteins in fasta format, or to create a codon usage table (“.bias”) from the results.

Translate All CDS Features in Folder

There is a new Database | Translate All CDS Features in Folder menu option that is similar to Translate All CDS Features except that it prompts for a source folder and then loads every sequence file in that folder and translates each CDS feature that it finds, accumulating the results and offering the same result options as Translate All CDS Features. A codon usage viewer window is automatically created and displayed when you select this option (see below).

Codon Usage Enhancements

MacVector now includes a simple viewer for codon usage “.bias” files. This displays the data in a standard text format with one row of data per codon, identical to the codon usage output windows used in other MacVector translation functions. New From Clipboard will create a new .bias viewing window if text on the clipboard adheres to this format, or to the popular “GCG” format available on codon usage websites such as CUTG (http://www.kazusa.or.jp/codon/).

The viewer has a toolbar button for the Translate All CDS Features in Folder function described above. You can invoke this multiple times and each new set of results will be appended to the existing codon usage data. You can use this to slowly build up the codon usage information from a large sequence data set in multiple folder locations on your computer.

History Tab

There is a new tab in nucleic acid single sequence windows called History. This tab lists several MacVector-specific features relating to the editing history of the sequences such as ‘frag’ and ‘edit’. These features now contain additional information such as the date of the operation, the name of the user who performed it and additional sequence information. In the future, all MacVector sequence modifications will write out this information allowing the full history of any construct to be determined and even allowing a simple reversion of the construct to how it existed on a specific date.

Change in Default Restriction Enzyme File Location

By default, MacVector now stores restriction enzyme files in ~/Library/Application Support/MacVector/Restriction Enzymes/. Because this location is within the current user’s home folder, it will always be writeable, even if the user does not have Administrator access to the machine. Note that if you have already copied restriction enzyme files to a different location, then you will not be affected by this change and your original files will be unaffected

When MacVector starts for the first time, it will create and populate this directory with the latest set of restrictions enzymes shipped with MacVector. It will then look in the old /Applications/MacVector/Restriction Enzymes/ folder and if any files in there have a newer time stamp than the default enzymes, then those files will be copied to the new location, ensuring no user edits to the data files are lost.

Miscellaneous Enhancements and Bug Fixes

The Align to Reference SNPs tab now also displays the percentage of each residue present in each heterozygote SNP.

The Align to Reference consensus calling threshold default has been raised to 70% so that heterozygous SNPs are more consistently reported on the consensus line.

A crash when repeating heterozygote analysis has been fixed.

Copied fasta text data is now more reproducibly parsed as single sequence data by New From Clipboard.

The protein pI calculations have been modified to also report the pI ignoring Trp and Cys residues. This brings the results more in agreement with the popular ExPASY website.

A bug where the “blocking” for protein sequences was taking the DNA values has been fixed.

Exporting sequence data in the Sequin .tbl format now correctly writes out the correct sequence for the minus strand of segmented features.