What's New in MacVector 14.0?
There are two main changes to MacVector with this release. Most importantly, MacVector 14.0 is now a 64-bit application - this allows much larger sequences and alignments to be analyzed and also helps future-proof MacVector against changes in Mac OS X. There is also a new "Primer Database" concept that allows you to easily maintain a database of primers and quickly search any sequence for potential binding sites.
The Assembler add-on has been updated with a new version of the popular Bowtie algorithm that handles insertions and deletions, making it far more suitable for use with longer reads.
As ever, there are a huge number of minor tweaks and improvements designed to simplify and improve workflows or to speed up common operations. You can download the full set of Release Notes here
MacVector is now a fully 64-bit application. The main utility of this is that MacVector can take full advantage of all of the memory installed on your computer, allowing it to handle larger sequences and alignments. This is most noticeable in the Multiple Sequence Alignment, Align To Reference and Assembler functions where longer reference sequences and increased numbers of (e.g.) fastq-formatted Reads can be imported and aligned. As an example, the Align To Reference interface can now import and assemble over 2 million fastq formatted reads against an E. coli genome in around 2 hrs on an iMac computer with 16GB of RAM.
The move to 64-bit has also allowed much longer sequences to be viewed in the Align To Reference editor – previously, sequences would not display properly when scrolling horizontally past about 2,000,000 base pairs.
MacVector14 is also no longer dependent on the deprecated “CarbonLib” compatibility library. This helps ensure that MacVector will continue to work with future releases of OS X where this library is likely to be removed.
Primer Database Support
MacVector now directly supports the concept of a “Primer Database”. There is a new Primer Database.nsub file installed in the /MacVector/Subsequences/ folder, populated with a number of common universal primers. This is used as the default database file, but you can easily choose any file of your own, or add your own primers to this file, or to a copy of it. The Analyze menu has been streamlined to remove the old Primers submenu.
Primer Database Search – this is a new function in the Analyze menu. Its is similar to the Nucleic Acid Subsequence search function, except that it uses Primer Database.nsub as the default search file and has extra settings to simplify handling primers with tails and/or mismatches to the target sequence.
Quicktest Primer – this now lets you save primers direct into the current primer database and also lets you retrieve primers from the database via a simple popup scrolling menu. In addition, this interface now handles primers up to 200 nucleotides in length.
Primer Design (Primer3) – you can now select primers in the spreadsheet result window and add them to the primer database and select primers from the database using the popup scrolling menu.
Additional changes have been made to the graphical representation of primer binding sites in both the Primer3 and Primer Database Search results so that the actual sequence of the primer (complete with mismatches and/or tails) is displayed ehwn zoomed to the residue level and if you select and copy the product graphic, the actual product sequence is placed on the clipboard which you can paste into a new document.
Installation and Use Without Administrative Access
This is the first version of MacVector that can be completely installed, licensed and used without requiring Administrative access to the machine. While primarily designed to simplify temporary "trial" evaluation, this does have some advantages for sites that need to restrict Admin access for users: many of MacVector's algorithms require "auxiliary" data files (e.g. Restriction Enzyme ".renz" files, or the new "Primer Database.nsub" file) and it is often useful to be able to write to these files, to change selections or to add new entries. By installing MacVector to the User's own home folder, these files are writeable by the user, simplifying their use.
Restriction Enzyme Methylation Sites
All of the enzyme files have been updated to include methylation information. The way this works is that there is both an (e.g.) XbaI and an XbaI-DAM representing the subset of Xba sites that are blocked by methylation. So if an XbaI site is displayed on a map with an XbaI-DAM site immediately above it, you know that site will be blocked by the Dam methylase.
Assembler Bowtie Improvements
Bowtie has been updated to version 2 which can handle gaps in the aligned reads or in the reference sequence. This allows the use of much longer input reads (which typically have more indels) and provides far more accurate coverage information because, with the older version, reads with indel mismatches would be discarded even if they were "real" matches. The output Map tab has been updated to display SNPs and "INDELs" graphically. Additional improvemnets have been made to the Summary, SNPs and VCF tab results.
The Primer Design (Primer3) “Test” mode now has a text output similar to the old Test PCR Primer Pair functionality, allowing you to view details of all of the possible products generated by the pair of primers.
There are some cool new "Rounded Rectangle" feature graphics types.
You can now directly select residues in the Map view in the default "zoom" mode. This lefts you use the Map tab for all editing operations except for actually typing residues (but you can select then click on the Editor tab to do that).
MacVector now supports the new Regulatory GenBank feature type.
You can import features into a sequence with files formatted using the Sequin Table format.
More options in the way the sequence Editor and Map views are initialized are now saved to preferences so that MacVector “remembers” how you like to view your sequences.
The cut sites and recognition sequences of restriction enzymes and now listed in the text outputs.
Colored residues or background in the single sequence Editor tab are now only displayed if the underlying feature is located on the sequence line. This provides much finer control over which regions of the sequence you would like to see highlighted in color.