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.
Miscellaneous Changes
Features
There are a wide variety of additional bug fixes and changes within MacVector 9.0, including significantly speeded up graphical displays, BLAST interface improvements, enhanced importing of VectorNTI sequence files and support for FastA files in the Align to Folder function.
Version 8.1
NCBI BLAST
Feature
The NCBI BLAST code has been completely rewritten to take advantage of the newer QBlast API.
Benefit. All connectivity takes place using standard web-style http communications In practice, this means that MacVector is now far more firewall friendly – previous versions of MacVector frequently required ports to be opened in the firewall for blast to work correctly – this is no longer necessary.
Job Manager
Feature
MacVector now has a Job Manager that is accessible from the Windows menu. Blast jobs can now run in the background.
Benefit
You can continue to work with MacVector while Blast jobs are in progress. You can also submit additional blast jobs without waiting for existing jobs to complete. You can monitor the status of jobs and stop them at any time from the Job Manager Window. If a job completes while you are working in a different area of MacVector, or in a different application, you will be notified by a bouncing icon in the dock (OS X only).
Version 8.0
Sequence Confirmation
Feature
MacVector now allows users to assemble one or more trace files against a reference sequence. The assembly is fully editable and users can directly invoke any MacVector analysis on the edited reference sequence.
Benefits.
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
Feature
MacVector now understands the sticky ends produced by cleaving DNA with restriction enzymes. It only allows users to paste restriction fragments into a vector if the ends are compatible. It also allows automatic flipping of fragments with different end structures if appropriate and manual flipping during pasting by holding down the shift key.
Benefits.
This prevents users from inadvertently creating biologically invalid molecules. There is an override option so that users can ignore the warnings if they wish.
Version 7.2
Chromatogram (Trace) File Support
Feature
MacVector can now read, write, edit, and analyse chromatogram files from automated sequencing machines.
Benefits.
This lets users run analyses, including alignments
and databases searches, directly on the source files from sequencing machines.
This not only saves time, but also lets users view the traces with the
sequences, letting them instantly see if unexpected results are due to errors
in the raw sequencing data.
Feature
Restriction Enzyme sites in the Map display are now live. Selecting one site positions the cursor at the cut location for that enzyme. Holding down the shift key and selecting a second site selects the entire sequence between the two cut sites. The selection can then be directly copies from the map view and pasted into a second molecule through a selection made in its map view, or in the editor view.
Click Cloning Support
Benefits.
This dramatically simplifies Click Cloning in MacVector. Users can document cloning constructs they have made by simply selecting the Restriction Enzyme(s) they used in the actual experiment,
copying, then pasting into the target molecule. All features in the copied fragment are transferred into the new molecule. In addition, all metadata associated with a feature (color, font, visibility, position etc) is also copied, making it extremely easy to maintain a standard reference appearance
for a large series of related constructs.
Version 7.1
OS X Support
Feature
The installer and application now run natively under OS X
10.0 and later.
Benefits.
The primary benefit is that OS X users do not have to switch to the ÒclassicÓ environment to run MacVector. Other benefits are; (a) no more memory limitations – OS X uses a virtual memory model that facilitates whole genome analysis (b) better multi-tasking (c) more attractive interface – check out the new 128 pixel square file icons and anti-aliased text.
Version 7.0
Phylogenetic Analysis
Feature
MacVector can generate and analyze true phylogenetic trees, using a variety of methods, including neighbor joining and bootstrapping. The phylogenetic analysis has a simple user interface, and is integrated with the multiple sequence alignment editor for maximum flexibility – letting you choose which sequences and which positions in the alignment will be included in the analysis. The results are presented in a variety of tree formats. The new Tree Viewer window allows you to analyze phylogenies interactively, and to fine-tune the display for publication-quality output.
Benefit
Makes MV very attractive to evolutionary biologists. Rather
than have to use many different applications to collect, edit, align, analyze
and publish the relationships between sequences, they can now do it all very simply in a single
program. They can very easily do ‘what if’ experiments with different alignment
and analysis parameters without needing to transfer data between incompatible
applications.
Full Featured Multiple Sequence Alignment Editor
Feature
Originally designed to view and modify the results of ClustalW
alignments, the multiple sequence alignment (MSA) editor in MacVector 7.0 has
been developed into a general-purpose multiple alignment tool. You can now
create empty MSA documents, or import alignments from other applications. You
can insert and delete sequences; insert, delete and modify residues; and copy
and paste parts of a sequence or blocks of an alignment. The controls for the
alignment display are now grouped on a single tabbed dialog box. You can use color
to indicate levels of similarity shown at a position, as well as to group
residues by their chemical properties. Users can now control every aspect of
how consensus sequences are calculated. In addition, the MSA editor allows easy
access to phylogenetic analyses.
Benefit
MacVector now offers the most comprehensive, flexible and
easy to use editor for multiple sequence alignment bar none. If users are using
anything else, they are working with one hand tied behind their back.
New Algorithms for Coding Preference Plots
Feature
New algorithms have been added to help you distinguish more
clearly between coding and non- coding regions of a nucleotide sequence. These
include G+C % composition analysis, three algorithms from Staden, and the
Wisconsin Package codon preference algorithm. You can select from a menu of
Open Reading Frames and coding analyses, and see all the graphical results
aligned in a single window. The controls for color and appearance of the
display have been improved, and locations of start, stop and rare codons are
included. The display is interactive, so that clicking on a start codon or ORF
will highlight the corresponding residues in the sequence window.
Benefit
Makes MV the easiest tool to use for manually identifying
protein-coding open reading frames in DNA. If users are attempting to annotate
newly sequenced DNA with the positions of likely open reading frames, this is
the simplest and most intuitive way to accomplish the task. While not suitable
for high throughput automated sequence analysis, this gives users much more
control and visual feedback over the identification of likely coding regions in
sequenced DNA.
Gapped Blast Searches
Feature
MacVector 7.0 can access NCBI’s enhanced BLAST 2.0 programs,
and use gapped alignment with its blastn, blastp, blastx and tblastn programs.
Benefit
Gapped alignment yields results that are more biologically
meaningful than those of ungapped alignment.
Transcription Based on Exons or Other Features
Feature
Users can now easily generate a translated protein from a
DNA sequence that includes non- coding intron regions. The new Transcription
Analysis functionality allows users to use features of a sequence to determine
which parts will be transcribed to mRNA. You can generate a transcript by
specifying a single coding sequence, one or more exons, one or more introns, or
one or more RNA features.
Benefit
This feature makes it simple for user to download a genomic
sequence containing a coding region and quickly create a messenger RNA from the
gene. It saves time, confusion and errors attempting to select individual exons
and combine them together in a basic sequence editor.
Enhanced File Input.Output
Feature
MacVector’s ability to handle data generated by other
applications has been extended, with new support for the import and export of
EMBL and SWISSPROT feature tables, and for importing and exporting data in
NEXUS, PHYLIP, NBRF and GCG-MSF multiple sequence alignment formats.
Benefit
Combined with the enhanced MSA editor and the Phylogenetic
Tree functions, this makes MacVector the leader in user friendly analysis and
editing of multiple alignments. Users can take pre- aligned data from any
standard source and display, edit and/or print the alignments with complete
control over colors and consensus calculation.
Enhanced Codon Bias Table Generation
Feature
MacVector can now generate more accurate codon bias tables
from GenBank sequences. A genome type filter has been added, to help ensure
that the most appropriate sequences are used to generate the codon bias table.
Benefit
This allows users working on relatively obscure organisms to
create specific tables to help with the identification of protein coding
regions. Combined with the new enhanced Coding Preference Plots, this makes MacVector
one of the most versatile tools for manually identifying potential coding
regions in newly sequenced DNA.
Modern File Navigation User Interface
Feature
MacVector 7.0 uses Apples new Navigation Services dialogs
when running on MacOS 8.5 and later. Navigation Services offers resizable file
lists, shortcuts for commonly used folders, and the ability to open several
files at once.
Benefit
This allows users to more easily navigate the Macintosh file
system, including support for favorites and most recent files. In addition,
users can select multiple files using the Navigation Services which greatly
enhances interaction with the Multiple Sequence Alignment Editor and ClustalW
alignments.
Enhanced Usability
Feature
Various enhancements have been made to the usability of MacVector
in version 7.0, including an improved Entrez interface with a more informative
and adjustable display, more rational setting of the DNA/RNA attribute, and
easier resetting of defaults in many dialog boxes. In addition, MacVector 7.0
handles large sequence files better, with the removal of length limits on
folder alignments and Pustell matrix analyses.
Benefit
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
Publication Quality Graphics
Feature
The user can completely customize the appearance of individual features and results. Attributes such as shape, color, shading, label text, font and location can all be set on a feature by feature basis. Maps can be viewed using any arbitrary scale and printed to any standard Macintosh printer. Feature maps and result maps can be saved as PICT or EPS files that can be used in Microsoft Word or graphics programs such as PhotoShop, Illustrator, PageMaker, and PowerPoint.
Benefit
This lets users create publication quality graphics directly
in MacVector, without having to create them by hand in a third party
application. Even if the supplied graphic options are not quite as users would like, they can easily export them to other applications, retaining all of the formatting and appearance they carefully created in MacVector. This not only saves time and the need to purchase expensive third party software (e.g. PhotoShop or Canvas) but also presents an attractive interface to users that makes it easy to identify features of interest.
User-Defined Primer Testing
Feature
Primer sequences can be entered and tested for usability as
PCR or sequencing primers against a template sequence. MacVector tests the
primer for secondary structure formation and also indicates the primerÕs Tm,
%GC and the region where it binds on the template sequence.
Benefit
Users can now immediately scan their own primers for
secondary structure, Tm and interfering binding sites on a target sequence.
This saves them time and money by screening out primers that are likely to have
problems before they order them and perform the actual experiments.
New Protein Tools
Feature
A number of algorithms for protein analysis have been added
to MacVector 6.5, including: Argos transmembrane helices, von Heijne
hydrophilicity, Fauchere-Pliska hydrophobicity, Janin hydrophobicity, Manavalan
hydrophobicity, Sweet-Eisenberg hydrophobicity, Parker antigenicity, Protrusion
Index (Thornton) antigenicity and Welling antigenicity.
Benefit
This provides users with an easy to use interface to
algorithms that can help to predict the function and cellular location of
proteins. Although many of these algorithms are available over the Internet, MacVector
pulls them together into one place where the results of different algorithms
can be directly compared. The user saves time and can use algorithms that they
may not be aware of or that would require multiple submissions over the Internet.
Flexible Property Profiles and Composition Analyses
Feature
The new base composition plots offer the user the choice of colors
for the various mono-, di- and tri-nucleotides, as well as the choice of which
plots to draw together in the same graph. All plots are completely color
customizable and can be combined onto a single plot for easy comparisons. Users
can zoom in to areas of interest to locate interesting nucleotide regions with
a simple mouse click.
Benefit
This provides the most simple and user-friendly interface
available for examining base composition in a DNA sequence. The flexible
graphic presentation allows users to easily identify regions of a sequence that
might be important for protein coding, transcription regulation or chromosome structure.
No other interface permits such easy mouse navigation and viewing of these
nucleic acid properties.
Color Printing for ClustalW Alignments
Feature
The ClustalW multiple sequence alignment
editor can now be printed in color, allowing the user to present results more
clearly. Alignment results can easily be incorporated into posters,
presentations and memos.
Benefit
Users can print attractive full color what-you-see-is-what-you-get outputs of their alignments with flexible color coding of sequence similarities and identities. No other package offers this
capability.
Dendrogram Output for ClustalW Alignments
Feature
The results of a ClustalW multiple sequence alignment can be viewed in a variety of ways, the newest of which is the dendrogram. The dendrogram can be viewed as a phenogram or a cladogram, and the user can
customize its appearance.
Benefit
Users get a quick and dirty estimate of the relationship
between their sequences. While not a substitute for a full-blown phylogenetic
analysis (see MacVector 7.0) this does allow users to narrow their field of
interest to the most closely related sequences and save time pursuing weakly
related leads.