Major release details – Summary

(See here for a detailed history of the last releases)

MacVector 18

Overview

MacVector 18 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. Plus 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.

Support for Additional File Formats

MacVector 18 wil import:

  • SnapGene .dna files
  • xdna files from Serial Cloner
  • Sequencher projects
  • Enhancements to Outlining Shared Domains in Aligned Sequences

    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.

    Trim by Quality

    Both the Align to Reference and Assembly Project windows now let you trim reads based on quality.

    Miscellaneous Enhancements

    There have been a large number of minor enhancements to smooth out workflows and improve compatibility with the macOS and other applications. In particular, MacVector 18 now includes embedded versions of Python and Perl as recommended by Apple.

    MacVector 17.5

    Outlining Shared Domains in Aligned Sequences

    Multiple sequence alignments now retain feature information and can use this to outline shared domains in the Picture output tab.

    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.

    Contig and Align to Reference Editor Enhancements

    There have been a number of enhancements to these editors.

    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.

    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 to Delete Clipped Residues and Close Gaps by Deleting Residues. You can also Nudge reads in an alignment

    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.

    Scan For… Missing Primers
    Automatically scans for and displays primer binding sites from your own Primer Database.

    Restriction Enzyme Picker
    A new compact interactive interface for selecting and filtering Restriction Enzymes to simplify the identification of useful enzyme cut sites in your sequences.

    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/Ligase-Independent Assemblies
    Automatic primer design and assembly of constructs for Gibson Assembly or Ligase Independent Cloning methods, complete with the effects on CDS translations.

    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
    Identify 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. MacVector now supports those APIKeys

    Miscellaneous Changes

    You can now copy and paste features between sequence documents.

    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.

    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.

    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.

    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

    A new BLAST results tab 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. For each hit, you can choose to download the entire sequence, or just the aligned segment plus ~2kb either side.

    Automatic ORF Display

    MacVector now automatically searches for open reading frames in every DNA sequence that you open. 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.

  • 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
  • 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

    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.

    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.

    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.

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

    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

    Agarose Gel Simulation MacVector 14.5 introduces a photo-realistic agarose gel simulation with recreations of restriction digests of linear and circular molecules under a variety of electrophoresis condition.

    Align To Folder now handles paired read files.

    Reduced Memory Footprint: for all editors but especially for Align To Reference alignments against large fastq files.

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

    Documenting cloning procedures Fragments on 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.

    Version 14

    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.

    Primer Database Support MacVector now directly supports the concept of a “Primer Database”. All primer design tools can use or save directly from the primer database.

    Primer Database Search: scan sequences against the primer database.

    Installation and Use Without Administrative Access MacVector that can be completely installed, licensed and used without requiring Administrative access to the machine.

    Restriction Enzyme Methylation Sites All of the enzyme files have been updated to include methylation information.

    Assembler Bowtie Improvements Bowtie has been updated to version 2 which can handle gaps in the aligned reads or in the reference sequence.

    Primer Design – Test” mode now has a text output similar to the old Test PCR Primer Pair functionality, with details of all of the possible products generated by the pair of primers.

    Version 13.5

    Align To Reference now handles alignments around a circular sequence and will export mapped reads in fastq or fast format.

    Align To Folder can now perform alignments against fasta and fastq files and outputs matching reads in fasta or fastq format.

    Pustell Matrix (“Dot Plot”) Enhancements: The performance of large (i.e. genome-sized) Pustell Matrix dot plot alignments has been dramatically improved.

    Assembly Coverage report Reference alignments now have a separate coverage report tab that lists the read coverage for every gene and CDS feature in the reference sequence.

    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.

    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.

    Version 13

    Quicktest Primer and Restriction Enzymes 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.

    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.

    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.

    Tabbed Results windows The results from every analysis of a sequence are tabbed to stop window clutter.

    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.

    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, generate new constructs and have full control over the appearance of features. Entrez and BLAST are still available along with the Find functionality.

    Cloning Clipboard

    simplifies the creation of new DNA constructs. The new functionality lets you join molecules together using an intuitive drag and drop interface. 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 allowing you to now run pairwise alignments of whole genomes in just a few minutes.

    Align To Reference Performance Enhancements

    optimized to be of more use for aligning large numbers of Next Generation Sequencing reads against large genomes.

    Optimized Reverse Translations allowing you to optimize codon usage when reverse translating a protein.

    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.

    Import annotation from Genome Browsers 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 existing Assemblies Import BAM/SAM alignments for displaying.

    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: supports Bowtie assemblies of Fastq datasets. Collections of contigs can be exported in FastQ format for additional analysis. 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.

    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.

    Version 12.0

    Licensing:introduction of Personal licenses and Network Roaming Licenses.

    Circular Sequence Support: Selecting across circular origins

    Map View Enhancements: Double-stranded sequence display. 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

    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

    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.

    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.

    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.

    One Comment

    1. mariam abdelmalak
      Posted March 9, 2020 at 1:08 pm | Permalink

      I need to download mac on my computer

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