Optimizing analysis parameters from the results window

The majority of MacVector’s analysis tools use a standard workflow:

  • Make sure the sequence you want to analyze is the frontmost window.
  • Select the analysis function from the Analysis Tools toolbar or from the Analyze menu.
  • A setup dialog appears letting you assign the parameters to be used in the analysis.
  • The algorithm runs and then a Filter dialog appears, letting you choose which outputs you would like to see and optionally apply filters so that only a subset of the results is displayed.
  • Result windows are then opened in a tabbed results window which you can typically interact with.
The Setup dialog shown for the Restriction Enzyme Analysis tool

Optimizing results

Once you have run the initial analysis then for subsequent analysis you can just repeat the analysis you have just done and further filter it. To do so you need to rerun the analysis tool except now select the Results window (at the tab showing the results you want to optimize) instead of the original sequence.

Restriction Enzyme Analysis

For example for Restriction Enzyme analysis the Filter dialog allows you to further refine the restriction enzyme recognition sites found, for example if you started with a broad search but now want to just show sites that are cut a certain number of times, leave a 3′ overhang or 5′ overhang, have a recognition site of a certain length or other filters. This is also useful if your initial search was too stringent and did not find any sites.

The Filter dialog showing many matches as the Setup dialog had a broad criteria
The Results window showing the many restriction enzyme sites that meet that broad criteria.
Rerunning the RE Analysis tool but now from the Results window.
The results after changing Number of Cuts to 1 and only selecting enzymes with a 5′ overhang.

Primer Design

Some tools work slightly different. For example Primer3 will just show you the filtering dialogue with just output options but without any filtering options (as all options are in the initial setup dialog). But you can just click “RUN AGAIN” and the Primer3 setup dialog is shown with the settings exactly as the subsequent run with the same sequence range selected.

Select the Try Again button to repeat a Primer3 analysis from the Results window
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MacVector 18.7.5

As an early Christmas present we’ve just released MacVector 18.7.5. There’s no new features but quite a few bug fixes especially with a few crash and performance issues with scrolling large alignments.

Either wait to be automatically promopted to update. Go to MACVECTOR | CHECK FOR UPDATES… or download manually.

Happy Holidays!

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Happy Holidays from the MacVector Team

We hope 2024 was a productive and enjoyable year for your research, and that MacVector played some part in that.

During 2024 we released MacVector 18.7 with the History Tab to view the history of your sequence and also tools to generate and import Codon Usage tables. We also merged Assembler with MacVector to give all active users the tools to assemble their own sequencing datasets with Assembly Projects.

Before you shutdown the DNA sequencer and close your pipette tip boxes, help your colleagues make the most of MacVector and give the gift of MacVector Weekly Tips) for Christmas. We curate these tips from the most common support calls and emails that we receive. Please encourage any of your colleagues who use MacVector to sign up. It only takes a few seconds, but the gift lasts all year. They will only receive a MacVector Weekly Tip email once a week and we never pass on email addresses to third parties.

We hope you are able to take some time off over the next few weeks to spend with family and friends. 

We wish you a happy and healthy New Year!

Expect some great new analysis tools from MacVector in 2025!

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MacVector Pro is now MacVector Pro with Assembler

MacVector Pro now includes Assembler, a powerful sequence assembly plugin that brings sequence assembly directly to your desktop with the same user-friendly interface MacVector users have come to expect. Assembler simplifies the management, assembly, and analysis of all types of sequencing data.

Assembler’s extensive toolkit has always been seamlessly integrated into MacVector, but previously required an additional purchase. In response to the growing availability of sequencing data and to better serve our customers, we have made the decision to include Assembler at no extra cost for all active MacVector users starting in September 2024.

Assembler combines the Assembly Project manager with a robust sequence assembly toolkit, offering features to handle a wide range of sequencing reads from various platforms. From Sanger reads to PacBio and Nanopore long reads. With six de novo assemblers and two tools for mapping reads to a reference sequence, Assembler provides the necessary tools for efficient and accurate assembly. Users can even perform de novo assembly of genomes up to ~100 Mbp on a standard Mac laptop.

How to upgrade your license to MacVector with Assembler

  • Active users: on your next renewal date Assembler will be automatically added. You do not need to do anything (alternatively contact MacVector Support now).
  • Inactive users: request an upgrade quote and Assembler will be included at no extra cost.
  • New licenses: Assembler will be added to all new licenses.

With MacVector and Assembler you no longer need a powerful Linux server for sequence assembly.

Assembler is fully integrated into MacVector and allows you to manage sequencing data with the familiar MacVector style. You can design primers directly on a contig or BLAST that contig to identify it.

de novo sequence assembly using Phrap, Velvet and SPAdes with Flye for PacBio and Oxford Nanopore.

Reference Sequence Assembly: Map millions of reads against genomes, transcriptomes or other reference sequences using Bowtie2.

MacVector

Compare Genomes: Compare two related annotated genomes to see common or missing genes.

Coverage Tab: compare multiple assemblies with expression level comparison.

Variant Calling: SNPs and INDELS are visualised on your assembly and supplied in VCF.

Bacterial genome tools Tools for finishing bacterial genomes including circularizing genomes.

Easy to use interface. Navigating around your assemblies has never been easier. Display an entire contig in the graphical Map and select a read to zoom straight to that region. Click on a base in a contig and see coverage and variants.

MacVector

Heterozygote analysis. Analyse heterozygotes in Sanger trace files or assemblies.

Assembly Project manager makes it easy to assemble multiple datasets, reference sequences and assemblies. Work with unaligned reads from an assembly directly in the project.

Compare different assemblies. Map multiple datasets against the same reference, or repeat the same assembly with different options.

RNA-Seq analysis with read depth visualization and per gene coverage data (RPKM & TPM).

With MacVector/Assembler, there is no need to send your sequencing away or learn complicated software tools. You can analyze your own data with MacVector on your own Mac. 

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MacVector 18.7.3: a minor bug fix release

We’ve just released MacVector 18.7.3. This has a few minor bug fixes with calculating amino acid properties of a protein sequence:

  • Protein Analysis Toolbox hung on certain protein sequences.
  • A minor calculation bug in the pI calculation. The new results should more accurately reflect the actual mobility of proteins in a pH gradient gel.

If you have not yet been prompted to upgrade then go to MACVECTOR | CHECK FOR UPDATES… or download the installer directly.

MacVector 18.7.3 is fully supported on macOS High Sierra to macOS Sequoia.

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MacVector and macOS Sequoia

Apple released macOS Sequoia earlier this week (16th September 2024). As usual in the run up to a new macOS release, we have been testing MacVector on development builds of macOS Sequoia. We are happy to report that there are no issues and that MacVector 18.7 is fully supported on macOS Sequoia.

MacVector 18.7 running on macOS Sequoia

If you do come across any issues that we have missed (we do try but there’s always some bugs that hide until it’s too late!) please do contact support.

Compatibility of previous versions of MacVector

For versions of MacVector before MacVector 18.7 you can check compatibility on a table which we update after every new release of macOS and MacVector.

Basically MacVector 18.6.1 should work fine on macOS Sequoia although it is not officially supported. For earlier versions of MacVector then due to last minute changes that Apple made last year to macOS Sonoma there are many tools that will not work. Our developers strive to future proof MacVector, however, when Apple make significant changes this does sometimes take matters out of our control!

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MacVector 18.7 – View the history of your plasmid

The recently released MacVector 18.7 has a new History tab in the Single sequence editor that shows the editing history of your DNA sequences

Since the introduction of MacVector’s Cloning Clipboard, all cloning actions (such as ligating a digested fragment into a vector) create a /FRAG feature that records the source of the ligated fragment, the restriction enzymes used to digest it (and any end treatment such as Klenow) as well as a timestamp. Then with the introduction of the OPTIMIZE CDS (MacVector 18.6) feature this also creates a new EDIT feature that details information about the action.

The new History tab lists these “history” features along with a timestamp and user of when they were performed thus allowing you to track the edit history of your sequences.

Although currently there are only a few edit operations that store information in the History tab, eventually all sequence modifications will write out this information allowing the full history of any construct to be determined and eventually allowing a simple roll back of the construct to how it existed on a specific date. The history tab may be sorted according to the user and date as well as the usual sort columns.

The following edit operations are currently shown in the History tab.

  • CDS Optimization: creates an /EDIT feature.
  • Cloning operations: such as ligating genes into a vector, create a /FRAG feature.
  • SOURCE annotations: These are a mandatory Genbank feature that summarizes the length of the sequence, scientific name of the source organism, and Taxon ID number. Can also include other information such as map location, strain, clone, tissue type, etc., if provided by submitter. Note: Source features are a standard Genbank feature and do not include timestamp or user.

Unlike all other annotation/features EDIT and FRAG features are not standard Genbank nomenclature. However, if you need to export your sequence as “pure” Genbank you can use FILE | EXPORT | Genbank Flat (strict). This will remove all non standard terms and export a file that is 100% compliant with the Genbank specification.

How to view the EDIT history of your sequence.

  • Perform a ligation of a digested fragment from another sequence
  • Perform a codon optimisation of a CDS feature
  • Switch to the HISTORY tab of your sequence.

MacVector 18.7 was released in July 2024 and introduces a History tab to track the construction of your expression vectors and clones. It also includes direct support for Codon Usage Tables, creating custom Codon Usage Tables and batch translation of CDS features. Additionally, MacVector 18.7 enhances Assembler’s toolkit by adding a new reference assembler for mapping PacBio and ONT sequencing reads to your reference sequences.

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MacVector 18.7 – Change in Default Restriction Enzyme File Location

One change in MacVector 18.7, that will improve installation on multi user Macs, is that by default MacVector now stores restriction enzyme files in the user’s home folder. Since it’s the user’s home folder, it will always be writeable, even if the user does not have Administrator access to the machine. Additionally for a Mac used by multiple users editing these files will not affect other users restriction enzyme choices.

MacVector now stores RE files in ~/Library/ApplicationSupport/MacVector/Restriction Enzymes/.

To access this folder from Finder:

  • In Finder, hold down the OPTION key and click on the GO menu in the toolbar
  • Select LIBRARY and navigate to ApplicationSupport | MacVector | Restriction Enzymes

If you have already copied restriction enzyme files to a different location, then you will not be affected by this change, and your original files will be unaffected. When MacVector starts for the first time, it will create and populate this directory with the latest set of restrictions enzymes shipped with MacVector. It will then look in the old /Applications/MacVector/Restriction Enzymes/ folder and if any files in there have a newer time stamp than the default enzymes, then those files will be copied to the new location, ensuring no user edits to the data files are lost.

If the files are missing?

If any of the Restriction Enzyme tools complain of no files, then do one of the following actions:

  • In the RE tool click DEFAULTS and the location will be corrected
  • Click SET ENZYME FILE and navigate to the new location.

MacVector 18.7 was released in July 2024 and introduces a History tab to track the construction of your expression vectors and clones. It also includes direct support for Codon Usage Tables, creating custom Codon Usage Tables and batch translation of CDS features. Additionally, MacVector 18.7 enhances Assembler’s toolkit by adding a new reference assembler for mapping PacBio and ONT sequencing reads to your reference sequences.

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MacVector 18.7.2

MacVector 18.7.2 update is now out

We’ve just released another minor update to MacVector 18.7. Sorry to follow an update with another update so quickly but we discovered two minor, but annoying bugs.

You will be prompted to update over the next few days (unless you have turned off update notifications). However, you can also run MACVECTOR | CHECK FOR UPDATES.. or download the new version directly

Changes for MacVector 18.7.2

Bug fixes

  • Filtering fastq reads in minimap2 could sometimes cause a crash
  • The button to turn of automatic restriction sites display was ignored and RE sites were always shown
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MacVector 18.7.1 update is now out

We’ve just released a minor update to MacVector 18.7.

You will be prompted to update over the next few days (unless you have turned off update notifications). However, you can also run MACVECTOR | CHECK FOR UPDATES.. or download the new version directly

MacVector 18.7 introduces the History Tab that documents how the sequence was constructed.

Changes for MacVector 18.7.1

macOS Support

This release now supports all macOS releases from macOS 10.13 (High Sierra) through
macOS 14.5 (Sonoma) and has also been tested on beta releases of the upcoming macOS
Sequoia operating system.

Bug fixes

  • Unique and non-unique restriction sites now correctly get updated to the appropriate color when inserting or deleting sequence data.
  • The minimap2 consensus calculation now includes quality information.
  • The minimap2 input parameters dialog now provides more intuitive enablement/disablement of parameters when the preset parameters menu is used.
  • The History tab now reports ‘source’ features as well as ‘frag’ and ‘edit’.

If your license is not valid for MacVector 18.7 please contact support.

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