General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Major Release Details: Detailed history of MacVector releases

MacVector 15

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.

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.

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