Major Release Details: Detailed history of MacVector releases

MacVector 18.5

Overview

MacVector 18.5 was developed and tested on macOS Ventura. It is supported on macOS High Sierra to macOS Ventura and is a Universal Binary that will run natively on Apple Silicon Macs as well as existing Intel Macs.

Heterozygote Analysis of Sanger trace files

The heterozygote analysis tool analyzes one or multiple Sanger trace files and reports on all possible heterozygotes.
You can also analyze Sanger trace files and permanently change the basecalled sequence with an IUPAC ambiguity code representing the called heterozygote.
The tool works on multiple trace files in the Assembly project manager or the Align to Reference editor.
You can also basecall heterozygotes in a trace file in the Single Trace Editor.

Align to Reference supports long reads

Long sequencing reads from PacBio and ONT sequencers can now be assembled in Align to Reference.

Miscellaneous enhancements

– Importing Sequencher project (.SPF) files has been significantly enhanced.
– As usual there’s been a lot of bug fixes and changes that you probably do not care about! But be assured that everything we do makes MacVector a future proof and modern macOS application that you can rely on!

MacVector 18.2

Overview

MacVector 18.2 is a Universal Binary that runs natively on both Apple Silicon and Intel Macs. It is supported on macOS Sierra (10.12) to macOS Monterey (12).

Align to Reference Enhancements

The Align to Reference alignment algorithm has been overhauled to do a much better job handling larger numbers of gaps in the alignment between a reference sequence and a read. Previously, for the standard alignment algorithm, more than 5 or 6 consecutive gaps in either reference or read would be poorly resolved. Now 20–40 consecutive gaps, such as might appear in CRISPR experiments are handled with ease, depending on settings. However, if you are expecting introns when aligning e.g. mRNA sequences versus a genome, you should still use the cDNA Alignment option which will also take splice site consensus sequences into account.

The alignment algorithm has been further optimized for speed and is now 2–10 fold faster depending on the sequences being aligned. In addition, the Sensitivity setting can now be lower due to the enhanced consecutive gap detection, which also speeds up calculations.

When aligning ABI chromatogram data, or plain sequences, the Map tab now graphically displays the “trimmed” regions at either end of the sequences making it far more obvious when there is only partial alignment between two sequences. This does not apply to NGS reads where it is impractical to view potentially millions of reads in the Map tab.

There is a new Remove Gaps context-sensitive (right-click) menu option that deletes residues in reads that correspond to a gap in the consensus sequence. This can clean up noisy assemblies where a low percentage of reads have extra residues inserted leading to a lot of gaps in the consensus sequence and a very cluttered display.

Context Sensitive Hamburger Menus

Many of the views and windows in MacVector have context-sensitive menus available when you right-click (or -click) in them. To make the availability of these options more obvious, these views now contain a “hamburger” button (three parallel horizontal lines) that displays the same context sensitive menu when clicked on. So, if you see the button on the toolbar, click on it to see what additional options are available.

Importing of Primer Databases in TSV or CSV Format

You can now directly import primer data into a MacVector Primer Database (.nsub) file. First, prepare your data in an Excel or Numbers spreadsheet with three columns – “Name”, “Sequence”, “Comment”. Then export the data (or Save As…) in Tab Separated Values format or Comma Separated Values format. Open the file with TextEdit, select all the rows of text, Edit | Copy, switch to MacVector and select File | New From Clipboard. This functionality replaces the old Primer Converter utility which no longer runs on modern macOS systems.

Miscellaneous Enhancements

To reduce clutter in the Assembly Project window toolbar, all of the assembly algorithms have been consolidated into a single Assemble toolbar button with a dropdown menu.

MacVector 18.1

Overview

MacVector 18.1 is a Universal Binary application that means it runs natively on Apple Silicon and Intel Macs.

Universal Binary

MacVector 18.1 is a Universal Binary, meaning that it can run natively on both Intel and Apple Silicon Macintosh computers. Other than the ability to run natively on M1 processors, MacVector 18.1.1 is essentially identical to MacVector 18.0.1 with the exception that the embedded Python framework has been updated to version 3.9. Currently, all of the embedded 3rd party algorithms are included as Universal Binaries with the exception of SPAdes and Bowtie – these run under Rosetta2 emulation on Apple Silicon machines. However, in our hands, they still out-perform equivalent older Intel- based computers.

Cosmetic Changes for Big Sur

The main application icon and window toolbar appearance have been updated to match the macOS Big Sur “look and feel”.

Improved Align to Reference SNP Reporting

The align to reference algorithm has been slightly tweaked to do a better job of aligning reads that have insertions relative to the reference. The SNPa tab has been revised to use standard reporting for both nucleic acid SNPs and for corresponding changes to amino acid sequences in CDS features. In addition, small deletions are now reported, again using standard nomenclature.

Misc

The use of a comma as the decimal point separator is now supported throughout MacVector for international localization. Import of GFF files has been improved.

MacVector 18.1 is fully supported on macOS Sierra to macOS Big Sur.

MacVector 18.0

Overview

MacVector 18.0 adds a number of new functions, including the ability to read several requested file formats such as Sequencher assembly project files along with Serial Cloner and SnapGene sequence files. There is a new CRISPR PAM sequence searching function and a Trim by Quality option for Sanger sequence files. Finally, there are major enhancements to the protein multiple sequence alignment visualization of domains and the usual macOS compatibility enhancements.

MacVector 18.0 is fully supported on El Capitan to macOS Big Sur. This release is not a native Apple Silicon build. However, MacVector 18.1 will be released very soon with full Apple Silicon Universal Binary support (ARM64 and X86_64).

Searching for CRISPR PAM Sites

A new tool Analyze | CRISPR PAM sites… menu item will scan Nucleic Acid sequences for Protospacer Adjacent Motifs associated with the CRISPR Cas9 and related enzymes cleavage and modification functions. By default, MacVector uses a file called Protospacer Adjacent Motifs.pam that is located in the /Applications/MacVector/Subsequences/ folder. It contains most of the current Dec 2020) characterized Cas9-like enzymes, but you can always open the file and add your own. While MacVector does not currently search genomes for potential off-target sites, this is still a very useful function to alert you to potential CRISPR target sites. The output is a mix between the current Restriction Enzyme and Nucleic Acid Subsequence searches, so you can easily see and copy the guide sequences. You can also have MacVector automatically scan for CRISPR PAM sites whenever you open a DNA sequence file – control this using the MacVector | Preferences | Scan DNA pane.
The results are shown in the Map tab, and you can zoom in to see the actual sequence of the hits with the guide sequence shown in lower case and the PAM sequence in upper case.

Support for Additional File Formats

You can now import SnapGene .dna files, complete with feature colors, and .xdna files from Serial Cloner, which is an extended version of the old DNAStrider format.
You can also import Sequencher projects into a MacVector’s Assembly Project.

Enhancements to Outlining Shared Domains in Aligned Sequences

First added in MacVector 17.5, this functionality has been significantly enhanced to expose additional Feature-related functionality in Multiple Sequence Alignment documents. There is a new Features tab in the protein multiple sequence alignment window where you can view, edit, create and/or delete features in each of the aligned sequences.

When the Editor or Picture tabs are active, a new floating Groups Palette is displayed (similar in concept to the Graphics Palette for the single sequence Map tab), allowing you to turn features on and off permitting greater control over how shared domains are displayed and outlined.

Trim by Quality

Both the Align to Reference and Assembly Project windows now let you trim reads based on quality. The reads (typically Sanger sequencing reads in ABI or SCF format) should not be aligned prior to running the algorithm. A typical workflow might thus be to add .ab1 or .scf files to a project, optionally base call with phred, if needed, then Trim by Quality prior to aligning or assembling.

Miscellaneous Enhancements

There have been a large number of minor enhancements to smooth out workflows and improve compatibility with the macOS and other applications. Some, such as reworking code behind the scenes to replace deprecated Apple functions and refactoring code for better stability and performance, help ensure that MacVector will continue to work on upcoming releases of macOS and take advantage of improved hardware. In particular, MacVector 18 now includes embedded versions of Python and Perl as recommended by Apple.

MacVector 17.5

MacVector 17 has a new domain-outlining facility for multiple sequence alignments, letting you more easily visualize the relationships between features in aligned sequences. There is a new algorithm (Flye) for de novo assembly of PacBio and Oxford Nanopore long reads and enhancements to the Contig and Align to Reference Editors, including coloring based on quality values and editing status. As ever there are a slew of minor enhancements, bug fixes and changes to better support the latest releases of macOS.

Outlining Shared Domains in Aligned Sequences

Outline shared aligned domains Multiple sequence alignments now retain feature information and can use this to outline shared domains in the Picture output tab. You can set the colors of features in the individual sequence documents in the usual way and these are used for the outlines.
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There is a feature display mode in the Editor tab where you can see the extent and color of the features. When you switch to the Picture tab, you will see colored outlines around the shared domains;

de novo Assembly of PacBio and Oxford Nanopore reads with Flye

Flye is an assembler algorithm tuned to assemble poor quality long reads such as those produced by PacBio and Oxford Nanopore sequencers. Because these reads tend to be very error prone, MacVector 17.5 also includes an optional polishing step using Racon. With typical bacterial genome assemblies it is fairly common to be able to assemble reads into a single full-length genome contig.

Contig and Align to Reference Editor Enhancements

There have been a number of enhancements to these editors, primarily to aid in visualizing edits and quality values and to “clean up” the visual appearance of alignments.

Residue Background Colored by Quality

There have been several changes to provide improved support for quality values of de novo contigs and reference assemblies.
A Shading toolbar button lets you turn on coloring based on quality and edited residues are visualized with a blue background. Edited residues are always given a phred quality value of 99 – these residues are given a blue background.

Base Calling with Phred

You can now directly run phred on Sanger sequencing trace files in the Align to Reference Editor by clicking on the Basecall toolbar item with the appropriate sequences selected;

Editing Enhancements

There are some new context-sensitive menu items in the Align to Reference Editor tab

Delete Clipped Residues – deletes any greyed-out (“clipped” or “trimmed”) residues. While these are ignored by the consensus calculation, some users prefer to delete them for a cleaner looking alignment.

Close Gaps by Deleting Residues – you’ll often see gaps in the consensus where one or more reads has an additional erroneous inserted residue. This menu item removes the extra residues from the read, cleaning up the visual appearance of the alignment.

*”nudge” reads * – Select the name of the sequence you want to nudge and use the left/right arrow keys to move it around. If you have problematic alignments where you need to physically insert residues or gaps, hold down the

Miscellaneous Enhancements

There have been a large number of minor enhancements. Some, such as reworking code behind the scenes to replace deprecated Apple functions and refactoring code for better stability and performance help ensure that MacVector will continue to work on upcoming releases of macOS and take advantage of improved hardware. There have also been improvements to Dark Mode support in many area and much better handling of the labels in crowded Map views.

MacVector 17

Dark Mode
MacVector 17 supports macOS Mojave’s Dark Mode. To aid concentration on those late night primer design sessions!

Scan For… Missing Primers

Automatically scans for and displays primer binding sites from your own Primer Database.Every sequence you open shows any binding sites from your lab’s freezer drawer primer collection

Restriction Enzyme Picker
MacVector 17’s brand new Restriction Enzyme Picker is a new floating tool for selecting and filtering Restriction Enzymes to simplify the identification of useful enzyme cut sites. It initially presents you with a list of all available sites in a sequence. However, you can filter on many attributes, such as number of cuts, 5’ or 3’ overhangs and blunt ends. What’s more is that you can take a set of cut sites from one sequence as the input to digests of other sequences for easier planning of construct workflows. The Restriction Enzyme Picker gives you an interactive way to quickly show what enzymes are present in your sequence.

Compare Genomes
Compares two related annotated genomes (or smaller sequences) to identify and list, in spreadsheet form, identical, similar and weakly similar features along with missing features.

Gibson Assembly and Ligase-Independent Cloning tool

MacVector 17 has a completely new tool for automated design of ligase-independent cloning strategies. The tool supports 5’ exonuclease driven Gibson assembly as well as the T4 DNA Polymerase 3’ exonuclease “Ligase Independent Cloning” approach. MacVector can automatically design primers when you specify fragments and vectors to use. You can provide custom primers (manually or from tools such as the NEBuilder website). You can also just provide existing fragments with overlapping ends for MacVector to assemble. The interface shows the exact structure of the junctions between fragments, including relevant CDS translations for confirming the frame of protein fusions. The cloning strategy can be saved as a new cloning project document and finally automatically assembled into a single sequence for export.

How Do I?
A new easy to access menu lists videos and simple tutorials to common workflows. Every tool dialog also has direct access to a simple video/tutorial on how to use it.

Assembly Problems tab
Idc sentify mis-assembled genomic sequences based on excessive mismatches, discontinuous reads and other common problems.

Coverage Tab
Compare different sequencing datasets assembled against the same reference sequence with expression level comparison.

Redesigned Assembly Project
Each assembly job creates its own folder for easier organization of multiple datasets, multiple reference sequences and repeated jobs.

Use of APIKeys with Entrez and BLAST
The NCBI have introduced a new system for accessing the Entrez database over the internet. They now throttle general accesses to the Entrez server to no more than 3 calls per second per IP address. This can be limiting if you are sharing a public IP address behind a company or university firewall and others are using MacVector. They have introduced a new “APIKey” concept – you can request one of these from the NCBI for your own personal use and that increases the permitted rate to 10 calls per second and is independent of the IP address. Thus, you can share a public IP address with colleagues and still each have the full 10 calls per second access.

Miscellaneous Changes

You can now copy and paste features between sequence documents. Simply select the feature in the Features tab of one sequence, Edit | Copy, then switch to another sequence Features tab and choose Edit | Paste.

You can now select a short sequence in a Read in the Align To Reference Editor tab, right-click to bring up a context sensitive menu, and then select all of the other aligned reads that contain that a sequence. It’s a great way of selecting all the reads with a specific SNP(s). Combine it with selecting the pairs for each read with NGS data and saving the selected reads and you have a very powerful way of analyzing SNPs or resolving repeat sequences in genomic assemblies.

Some of the nomenclature and interactions in the Primer3 dialog box have been cleaned up to simplify its use.

You can now add sequences to the Align To Reference window from multi-sequence GenBank files.

GenBank multi-sequence files now open by default as individual sequences.

When results are generated for the Bowtie Coverage tab, the name of each feature is now displayed exactly as per the label used in the Map tab allowing you more control over exactly how the text appears.

There is now an option in the Database | Auto-annotate Sequence… interface to automatically “fix” CDS features. This will change the stop location if the match creates a longer or shorter open reading frame and will also change the contents of any /translation= qualifier to reflect the new translated coding sequence.

The Align to Reference algorithm is now multi-threaded. You will see a significant speed up, particularly if you are using larger Sensitivity values, though we still recommend keeping Sensitivity to a low (less than 4) value and the Hash Value to the maximum possible value for optimal performance when searching through large amounts of NGS data.

MacVector 16.0

Scan for.. Missing Features.

Sequences are automatically scanned against a Common Features library and missing features are displayed. A simple right-click converts them to a permanent feature. Even blank sequences will be displayed fully annotated with common features. You can even add your own proprietary features to the Common Features library.

Batch Translation using Applescript

Produce individual protein sequence files, or FASTA files with all translated CDS regions from a folder of DNA/mRNA/cDNA sequences.

SPAdes: de novo assembly

This new algorithm offers support for mixed assemblies (e.g. Illumina, PacBio and Oxford Nanopore in the same assembly), has a smaller RAM footprint than Velvet and typically produces longer contigs.

Unified Feature Editor.

A new editor that combines the GenBank data and Symbol appearance into a single dialog for simpler editing.

Closing bacterial genomes

A new tool helps circularize bacterial genome assemblies by resolving ends where there are overlaps.

MacVector 15.5

Graphical BLAST Results

There is a new graphical BLAST results tab. It displays a graphical alignment of the query sequence aligned against each high scoring segment pair of the BLAST hits. This allows you to clearly see which genes or features your query is aligning to. If there are too many features to display in the graphical pane, simply hovering over it will expand to display all overlapping features. For each hit, you can choose to download the entire sequence, or, particularly useful for hits to entire genomes, just the aligned segment plus ~2kb either side.

This interface represents a new and powerful approach to quickly identifying the function of your query sequence. With the advent of NGS genomic sequencing, any bacterial query sequences in particular typically match entire genomes – this allows you to identify and download just the region that matches your sample sequence for further detailed analysis within MacVector.

Automatic ORF Display

MacVector now automatically searches for open reading frames in every DNA sequence that you open. This works similarly to the existing automatic Restriction Enzyme display. There is a new DNA Map tab in the main Preferences window that controls both of these functions;
Note that there is a checkbox (turned on by default) to suppress the display of ORFs that are already annotated on the sequence. In addition, the default appearance of ORFs has been changed to be less obtrusive in crowded Maps and they are now labeled with the length of the ORF.

You can quickly annotate the ORF to your sequence with a right mouse click.

Align to Reference: new tools

Many new tools have been added for simplifying the use of MacVector for closing the gaps in bacterial genome sequencing projects. Right click on selected reads to use them.

Export Consensus with/without Gaps

Align Selected Reads

Delete Selected Reads

Reset (unalign) Selected Reads

Export Selected Reads as FASTA/FASTQ

Select Matching Pairs (*)

Extend Reference with Selected Read (**)

() – if you have aligned a set of paired-end reads, you can select individual read(s) and use this function to select the corresponding mate(s). This is particularly useful if you want to find pairs that will extend a contig and export them for further analysis/assembly.
(*) This is active if you have selected a single read that hangs over either end of a Reference sequence. This will extend the Reference in the appropriate direction using the sequence of the read.

The Contig Editor has a subset of these functions with just the Export… and Select Matching Pairs functions available.

Miscellaneous Enhancements

Map windows now update when you change the default appearance of features.

A number of menu items have been renamed to more clearly explain what they do.

ORF results can now be filtered by minimum length.

A number of issues selecting different display options in the Phylogenetic Reconstruction tree display have been resolved.

MacVector now does a better job of interpreting complicated Bowtie alignments so that the alignment display has fewer out-of phase mismatches, whilst still retaining all of the residues in each read.

There is now an option to control the length of vertically oriented labels in the Map tab.

By default, only the main three NCBI databases are now shown in Entrez searches. You can ask to view more, but you may not be able to retrieve sequences from many of the others, other than through a browser.

MacVector 15.1

BLAST and Entrez

A complete rewrite of BLAST and Entrez to make them compatible with the new NCBI infrastructure. As of November 2016 only MacVector 15.1 and later will connect to the BLAST and ENtrez databases.

Misc.

Many bug fixes.

MacVector 15.0

MacVector 15 has new protein analysis tools for reference alignment of proteins, translated DNA alignments and for functional analysis of protein sequences.

InterProScan
Scan proteins for functional domains against a variety of sequence, protein family, domain and motifs databases (inc. UniProt, PROSITE, HAMAP, Pfam, PRINTS). Annotate domains to your sequence with a link to the database.

Multiple Sequence Alignment enhancements.

The Multiple Sequence Alignment tool has been improved with two new features. It will allow you to align DNA sequences based on their amino acid translations and multiple protein sequences can now be aligned to a single reference protein sequence.

Translated Multiple Sequence Alignments
Align DNA sequences based on their amino acid translations. Display DNA sequences and their translations at the same time. Align the protein sequences using ClustalW, Muscle or T-Coffee to see the effect on the underlying DNA sequences. Directly edit the DNA sequences and immediately see the impact of the change on the amino acid alignments.

Align proteins against a reference
You can use a protein sequence as a reference so that the display keys off that sequence when showing similarities. This allows you to view proteins in a similar way to the DNA Align To Reference interface.

Applescript and Auto Annotate
Auto-annotation has joined the growing number of MacVector tools that support Applescript. Batch annotate folders of blank sequences. Example scripts provided.

CRISPR Indel Analysis.
A new setting in the Align To Reference interface tunes the algorithm to more cleanly identify and display the short insertions and deletions that are frequently seen following CRISPR editing of a target.

MacVector 14.5

The main new feature in MacVector 14.5 is the addition of the Agarose Gel interface that lets you create photo realistic simulations of agarose gels. There have also been a number of improvements to memory usage so that it is now possible to create and manipulate much larger NGS alignments than with previous versions. Additional improvements include the ability to use the popular Align To Folder functionality against paired NGS data files along with a number of workflow enhancements to everyday functionality.

Agarose Gel Simulation

MacVector 14.5 introduces a new life-like agarose gel simulation window allowing you to view photo-realistic recreations of restriction digests of linear and circular molecules under a variety of electrophoresis condition. You just drag restriction sites from sequences and drop to show the migration pattern of a digest. For double digests you just select and drag two or more enzyme sites. Many different markers are available along with variations on agarose concentration and dye fronts.

Sequence Assembly Enhancements

Align To Reference Paired Read Awareness: There is now an option in the Database | Align To Folder function to handle paired read files. The paired reads must be in separate files and must reside in the same directory. If the appropriate checkbox is selected, MacVector will automatically work out which files represent pairs of reads, even if there are multiple sets of paired reads in the folder.

The main utility of this new functionality is that after the alignment has completed you can retrieve both reads of a pair into separate files using the Database | Retrieve To File function. Suppose you are looking to extend a contig from a de novo NGS assembly, or you are trying to pull out a gene from an RNA-Seq experiment based on weak sequence homology to a different gene;even if just one read of a pair matches the starting sequence, you can retrieve both reads into smaller fastq files which you can then use in additional assembly experiments to more efficiently extend alignments to cover entire genes or merge contigs.

Reduced Memory Footprint: This affects all sequence handling in MacVector, but is most noticeable when running Analyze | Align To Reference alignments against large fastq files. With MacVector 14.5, you can import much larger fastq files into these alignment windows – for example, on a laptop with 16GB RAM, it is now feasible to import upwards of 5 million NGS reads and align them to a reference sequence within a reasonable length of time.

Miscellaneous Enhancements

The Graphics Palette now contains a control displaying the current magnification factor and a stepper control allowing you to easily increase or decrease the radius of circular vectors.

You can now jump to alphabetically listed RE sites in the Results section of the Graphics Palette by typing the first letter of the name of the enzyme.

There is a new Edit | Remove Gaps function to remove gaps in single sequences and also in the Align To Reference and Contig editors.

The contents of the Cloning Clipboard can now be copied as a graphical PDF object – great for creating drawings in e.g. Adobe Illustrator outlining the derivation of a construct.

There are new Options | Fonts | Bigger/Smaller menu items that change the font sizes in most text-based windows. These include the Editor tabs, all of the plain text output windows and no also the table-based views (e.g. the Features and Annotations tabs). You can use [command[-“minus” and [command]-“plus” as shortcuts. Note you need to hold down the [shift] key to type “plus” as [command]-“equals” re-runs the last used analysis function.

The “Frame” option has been restored to the sequence Find function. This is particularly useful if you are looking for the location of specific codons in a coding region.

The Map tab has been reworked so that you can now “zoom” into a smaller region of a sequence without losing any existing selections.

Version 14

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.

64-bit Architecture

MacVector 14 is 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.

The move to 64-bit has also allowed much longer sequences to be viewed in the Align To Reference editor.

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.

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.

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 improvements have been made to the Summary, SNPs and VCF tab results.

Miscellaneous Enhancements

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.

Version 13.5

The graphics Symbol Editor and floating Graphics Palette have been rewritten in preparation for MacVector moving to a 64-bit architecture (due with MacVector 14.0). The other main enhancements have been aimed at better handling of Next Generation Sequencing (NGS) files, particularly with the Align To Folder and Assembler Velvet de novo assembly functionality. There has also been some code optimization to better handle the analysis of large genomic sequences, particularly noticeable with the Pustell Matrix “dot-plot” functionality.

Align To Reference Enhancements

Align To Reference now handles alignments around a circular sequence. Note that this is only the case for the “Sequence Confirmation” algorithm. The cDNA Alignment algorithm still assumes the target sequence is linear.

You can now select one or more sequence “Reads” in the Align To Reference Editor and save those reads to a fasta or fastq formatted file by choosing File | Export… and selecting the required format in the resulting dialog. In particular, this lets you run alignments of up to 500,000 NGS reads against a reference sequence and then specifically export all of the aligned (or non-aligned) reads for further analysis.

The cDNA Align To Reference algorithm now does a much better job of displaying segmented reads in the Map view.

Align To Folder Enhancements

Align To Folder can now perform alignments against fasta and fastq files with many millions of reads.

You can now retrieve the “hits” from an Align To Folder run to one of three destinations – the MacVector Desktop (i.e. opening each hit in a window on the screen), to a folder (where each hit is written out as a separate file) or to a single file (where the hits are concatenated into a single fasta or fastq file).

Taken together, these enhancements let you use Align To Folder to pull out rare matching reads from large NGS datasets for use in further analysis or DNA Assembly. In beta testing, this has been used to “clone” genes from MiSeq RNA-Seq runs using Protein source sequences aligned to Fastq data.

Pustell Matrix (“Dot Plot”) Enhancements

The performance of large (i.e. genome-sized) Pustell Matrix dot plot alignments has been dramatically improved. You can now scan and display pairs of bacterial genomes in just a few seconds to easily identify inversions, duplications and rearrangements in their gene organization. You can zoom in and out of the dot plot display in real time to explore the relationships right down to the residue level.

Nucleic Acid Subsequence Enhancements

A small but significant change has been made to the graphical output of this. If you select a pair of hits in the Map results tab, then choose Edit | Copy, the sequences of the actual subsequences are substituted into the copied sequence. This allows you to maintain primers in a nucleic acid subsequence file and use the Nucleic Acid Subsequence analysis option to quickly identify and “clone” predicted PCR fragments even if the primers have mismatches or tails added to them.

Assembler Enhancements

Reference alignments (from Bowtie) now have a separate coverage report tab that lists the read coverage for every gene and CDS feature in the reference sequence. You can use this to (e.g.) accurately measure relative expression levels of mRNA in RNA-Seq experiments or plasmid copy number in whole cell DNA sequencing experiments.

Velvet now does a much better job at trimming poor quality residues from input sequences.

Velvet now handles paired sequences that have identical names.

You can now export unassembled reads from Bowtie and Velvet alignments as fasta or fastq files. This lets you filter out reads that match specific sequences so you can focus subsequent alignments using a subset of reads.

Miscellaneous Enhancements

You can now reset the circular origin of circular sequences to any arbitrary position. Simply click between the residues where you want the new origin to be, then right-click (or -click) and choose Set Circular Origin from the popup menu.

Informative tooltips have been restored in all views.

A number of issues with saving trace files have been resolved. In particular, you can now use the bsml format to save annotations with chromatogram information.

Version 13

Quicktest Primer and Restriction Enzymes

The Quicktest Primer interface now displays 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 on the sequence along with ‘One out’ sites which are color coded to indicate whether they are silent mutations or not. Along with the new potential coding region if you introduce that change, and introducing that change is very easy. The display is interactive so that when you “mouse over” a site, additional information is displayed, such as the full cut site.

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 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. Double clicking on the site introduces that mutation to your primer.

Testing Primers

When you enter a pair of primers into Design Primers (Primer3) the interface switches to a new testing mode, TEST PRIMER PAIRS. At this point all parameters are relaxed so that your primers are always accepted.

A new enhanced summary page then shows statistics about your primers.

All reaction conditions are shared. so if you change [dNTP] in one tool they are changed and used for all other tools to achieve consistency of results.

De Novo NGS Assembly

Velvet has been added to Assembler for de novo assembly of 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 redesigned for easier visualization of multiple analysis. The output from each analysis is only dismissed when you want.The results from every analysis of a sequence are tabbed to stop window clutter. You can easily keep results windows open for many different sequences at the same time.

Applescript

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

Chromatogram enhancement

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.

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.

As well as the new interface the core of MacVector has been substantially rewritten to support future releases of OS X.

Version 12.7

MacVector Free

This is the first release with a free basic edition. Users can use MacVector Free to open or download sequences in any supported format, edit them, print, copy sequences, text and graphics, and save in any supported format. Users are able to 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.

Cloning Clipboard

A new Cloning Clipboard tool 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. This tool is great for designing and documenting subcloning from simple digests to complex multi fragment procedures such as Multisite Gateway. The history of every ligation event is recorded with the sequence showing the enzymes used, the date and any end modifications.

Dot Plot Performance Enhancements

Significant performance enhancements to the Dot Plot (DNA Matrix) analyses, allowing you to now run pairwise alignments of whole genomes in just a few minutes.

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.

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 that file.

Miscellaneous Changes/Bug Fixes

You can now create a feature “between residues” which can be displayed as a line graphic in the Map tab.If you subsequently select that feature the caret becomes positioned between the residues in the Editor tab.
Updated Short Protein Motifs.psub file. Thanks to Dr Peter Friedman, this subsequence file has been updated with many more useful entries.
Updated Gateway att sites. The att sites in the Gateway.renz and Common Enzymes.renz file have been updated to be more discriminating and to support newer att3, att4 and att5 vectors.
The installer is now signed with a MacVector, Inc certificate to prevent OS X 10.7 and later from warning that the installer is not from a trusted source.

Version 12.6

Primer Enhancements

A new QuickTest function allows easy design and analysis of primer sequences. You can view secondary structure in real time as you enter a primer sequence and add restriction sites or mismatches for site directed mutagenesis whilst viewing the modified translated sequence.

File input/export

Support of GFF, GFF3, and BED files to annotate blank sequences. Allows you to easily import annotation from Genome Browsers. Create new sequence(s) with complete annotations by copy and paste of GenBank, EMBL and FastA documents.

Assembler improvements

Major performance enhancements for displaying large assemblies.
Import BAM/SAM alignments for display.
de novo assemblies are now file based for larger assemblies. You can import ACE files for displaying alignments created by other assemblers. Child contigs are displayed as features on the reference contig, with interactivity between contigs so that selections in a child contig are reflected in the reference contig. SNPs, as reported in the VCF and SNP report pages, are displayed in the Reference Contig Map view.

Performance enhancements

Dot Plots (Pustell Matrix) can now handle small genome vs genome comparisons. For example a pair of E.coli genomes can be aligned in five minutes on an 2007 MacBook Pro. Major performance enhancements to Map Graphics for easier viewing of annotation rich genome sequences.

Version 12.5

Improved NGS support – The Assembler module has been rewritten to support Bowtie assemblies of FastQ data. Assembler can now support many millions of NGS reads and can generate output in the popular BAM format. Collections of contigs can be exported in FastQ format for additional analysis. The phrap interface has been enhanced to increase the number of reads that can be submitted for de novo assembly. Finally, the SNP detection and reporting has been enhanced with VCF output from Bowtie alignments and listing of all the codon and amino acid changes between the consensus and reference sequence alignments.

Extra alignment algorithms. Muscle and T-coffee have been added to the Multiple Sequence Alignment analysis interface, complementing the existing ClustalW algorithm.

Miscellaneous Changes

A number of older editors and lists (Restriction Enzymes, Subsequences, Scoring Matrices) have been rewritten in Cocoa, providing a cleaner interface and more selection and cut/copy/paste options.

Performance has been increased in many areas.

MacVector 12.5 will be fully Mac OS X 10.7 (Lion)
compatible.

Version 12.0

Licensing:introduction of Personal licenses and Network Roaming Licenses.

Circular Sequence Support: Selecting across circular origins – this has been a long standing limitation in MacVector – you can’t select across the origin of a circular molecule, so you can’t replace a segment there, or easily create features that span the split point. That will be fixed and you’ll also be able to rotate the molecule to any arbitrary split point.

Map View Enhancements: Double-stranded sequence display, New Symbol types – e.g. Full height rectangles, plain horizontal lines, plain lines with short vertical ends, single arrows with no drop to the sequence. Show CDS features as translations when at residue level, Show 3/6 frame translations of the sequence, Show Primer features as residues at residue level

Map View Navigation: Use arrow keys to nudge/slide through a selected segment (and have any results update appropriately), Navigable overview panel

Virtual Cloning: Show unique enzymes in unique color/font with compatible enzymes for left/right ends of a digested fragment highlighted in red/green. Show staggered RE cut sites in Map view when zoomed to residue. Show one out sites show in greyed out color with an asterisk next to name (e.g. EcoRI*).

Sequence Editor View: Allow users to change the case and color of the text in the editor, driven by the map view feature settings.

File Import: New From Clipboard option allows easy import of GenBank and EMBL formats

Sequence Annotation: Drag and Drop (or right click) to add results to a sequence as a feature

Miscellaneous Changes

Implement Align2Ref algorithm as a threaded job. Redesigned and rewritten Symbol Editor, Graphics Palette and Generate Transcript dialogues. Updated NCBI tools. Updated Genpept format, , Major rewrite for performance in drawing maps

Version 11.1

Workflow Enhancements: This release has a large number of changes designed to simplify and speed up many common workflows and to provide better integration
with the Macintosh operating system.

Multiple levels of Undo for the Multiple Sequence Alignment, Contig/Align to Reference and
Trace editor windows

Many analysis functions have been redesigned and (restriction enzyme, subsequence searches, translation etc) now use drop-down dialog sheets.

Other enhancements include the ability to import .ma4 files produced by Vector NTI, many tweaks to the graphics layout view (particularly for large sequences) and improved editing of Align to Reference and Contig Assemblies. In addition, there have been numerous bug fixes and underlying code cleanup so that MacVector 11.1
is more stable than ever.

Version 11.0

Auto annotation function that will scan a folder full of existing annotated sequences and automatically add matching features to your bare sequence.

Click Cloning has also become both easier to use and more powerful with the ability to manipulate overhanging ends and a new digest/ligate dialog. In addition, you can now display 3 or 6
frame translations directly below the sequence in the editor.

Assembler module has also been enhanced to provide support for next generation sequencing machines. Short read data may be imported in Fastq format and as long as you have a powerful enough Mac, de novo assemblies can be created.

Floating toolbar containing buttons for all common MacVector analysis functions. You can customize the toolbar to show just the functions you use most often or show
them all for rapid access to every available algorithm. You can even add any of the buttons to sequence window toolbars for quick access to your favorite
analysis algorithms.

Version 10.6

VNTI Database Support: Addition of Vector NTI database Browser MacVector, Inc. has just released MacVector 10.6. This release sees the introduction of a Vector NTI database import
function that allows MacVector to directly read sequence data from databases created by Vector NTI Advance v10 or earlier, even if the database resides on a Windows machine accessible over a network.MacVector 10.6 reads all of the standard features and annotations associated with each sequence. Also, since MacVector follows the Genbank format for the features table and is always kept up to date with the latest Genbank release, it has the added benefit of migrating any old and deprecated feature information contained in the Vector NTI file into the current nomenclature.

Miscellaneous Changes

Also included in MacVector 10.6 are enhancements and optimizations to the Align To Reference and Assembler alignment tools.

Version 10.5

Align To Reference. The Sequence Confirmation tool was renamed and now supports alignment of cDNAs to genomic sequences to aid in the identification of splice sites and introns.

Miscellaneous Changes

This version also builds on the new interface first introduced in MacVector 10, with customizable toolbars, a new multi-pane Preferences pane and popup menu paths on window title bars. File reading has been simplified and enhanced to allow easier importing of sequences into any function inside MacVector. Users will find more stability, better support for the OS X file system (including the use of long filenames) and a host of minor enhancements designed to simplify using MacVector under OS X. The Assembler module has been updated too, with easier editing of reads and contigs, and a new view to enable printing of contigs.

Version 10.0

Licensing: introduction of standard licensing to replace USB dongles

Dynamic Restriction Enzyme Analysis has had an interface overhaul with dynamic automatic restriction enzyme searching and display to simplify clone construction.

Feature editor to simplify the creation of GenBank style annotations has been added along with a redesign of the Entrez browser with support for more databases and retrieval of genomic contig sequences.

Primer design has also been updated with a new Primer3-based primer design function with support for real-time PCR primers.

Version 9.5

Universal Binary: will run on both PPC and Intel Macs.

Miscellaneous Changes

Improved graphics, updates to ClustalW for performing alignments on multiple core machines and a host of other improvements. MacVector 9.5 has been extensively tested on OS X 10.3, 10.4 and the upcoming 10.5 Leopard release.

Version 9.0

Feature.

MacVector 9.0 supports a new add-on module for sequence assembly. MacVector Assembler lets you assemble sequences using the industry standard phred, phrap and cross_match algorithms from the University of Washington and provides a full featured assembly editor with support for quality values. MacVector Assembler is tightly integrated into MacVector so that you can directly analyze the assembly with
any MacVector analysis algorithm.

Benefit

This lets you rapidly assemble and edit sequences using the most widely accepted sequence assembly algorithms directly on your Macintosh desktop. Outstanding speed, and tight integration with MacVector means that you can assemble, analyze and annotate sequences within the familiar MacVector interface.

This allows users to rapidly confirm the sequence of cloned fragments, PCR products, the junctions of cloning experiments or mutagenesis experiments. It also allows resequencing analysis of multiple clones/individuals and the identification of SNPs. This feature helps users from having to purchase a second dedicated application (e.g. Sequencher)for this purpose.

Sticky End Awareness

These enhancements make MacVector not only easier to use,
but also support the analysis of much longer sequences. This saves researchers
time and removes many of the frustrations present in other packages.

Version 6.5.3

Blast 2.0 Support

Feature

This was primarily a bug fix that allowed user to connect to
the Blast Ò2.0Ó server at the NCBI. The original Blast Ò1.4Ó server was
discontinued shortly after this release.

Benefits

. The new server provides better firewall
support than the old server, so there is a partial user benefit from this
release.

Version 6.5.1

Bug Fixes

Fragment
Map in restriction enzyme map option restored

Version 6.5