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 – Summary

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

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.

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