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!

Get ready for the release of macOS High Sierra with a 30% discount on all MacVector upgrades

macOS® High Sierra will be released Monday 25th of September. Whether you intend to upgrade early, or months later, you’ll be pleased to know that MacVector 15.5 (the current version) and MacVector 16 (our upcoming release) are both fully supported and compatible with macOS High Sierra.

  • If you are running MacVector 15.5. MacVector 15.5 is fully compatible and supported on macOS High Sierra. However, please do watch our Twitter, Facebook or blog for updates (and don’t forgot to backup! You spent a lot of time designing those constructs, don’t lose them!)
  • If you are running MacVector 13.0 to MacVector 15.0. Although these versions are not supported, we are not expecting any major issues. Please do contact support to check whether your license is valid for a later release (again backups are essential).
  • If you have MacVector 12.7 and earlier. You are strongly advised to either upgrade MacVector or not to upgrade to macOS High Sierra. There are significant problems with these much older versions.
  • During October we do have a 30% discount on all MacVector upgrades. So if you must upgrade to mac OS High Sierra and you are running an older version of MacVector then don’t miss out.

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    What can MacVector do for your lab?

    Here’s an overview of what MacVector 15.5 can do for you!

    Comparing sequences

    Whatever alignment your sequence needs, MacVector has the right tool.

    Cloning

    CRISPR Indel Analysis: Identify insertions and deletions following CRISPR editing of a target.

    Multiple sequence alignment of protein or DNA sequences using CLustalW/Muscle or T-Coffee and produce publication quality alignments.

    Sequence assembly of NGS data against a reference genome or sequencing of your new construct.

    Search for similar sequences in the NCBI’s Genbank database with your sequence using BLAST or search your own local set of sequences.

    Translated Alignments: Align DNA sequences based on their translations.

    Align proteins against a reference comparing known proteins against unknown ones.

    Characterizing sequences

    Auto Annotation of sequences with common plasmid features.

    InterProScan: Scan proteins for functional domains.

    Cloning

    Automatic ORF Display visualize open reading frames.

    Graphical BLAST Results Visualization of your BLAST search..

    MacVector

    Design Cloning workflows

    As simple as dragging a fragment to a cloning vector.

    Flexible Cloning Subclone with restriction enzymes, Gibson cloning, Gateway and more.

    Cloning history Every ligation in the construction of a plasmid is documented, wth enzymes used, any end modification, source of the fragment and date.

    Agarose Gel to run out digested sequences. Easily identify restriction site(s) to screen successful clones from incorrectly ligated inserts.

    Primer Design

    MacVector makes primer design both easy AND powerful.

    QuickTest Primer changes primer design. Hairpin? Nudge your primer until it goes.

    Add tails to your primers with silent restriction sites/mismatches and view reading frame changes.

    Quickly design pairs of primers click a region to get the best primer pairs to amplify it.

    Primer Database store your primers and scans sequences for potential binding sites.

    MacVector

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    NIH Research Festival 2017

    The MacVector team will be at the NIH Research Festival this coming Thursday and Friday.

    We enjoy the tent show and look forward to meeting NIH MacVector users both new and old, and anybody who is interested in learning to use the easiest to use sequence analysis application for the Mac.

    ORF AutoAnnotate

    Learn about the new ORF Auto Annotation added to MacVector 15.5 (our current release) or the Virtual Agarose Gel tool that we added a few versions back.

    We’ll be at Booth # 569, on Parking Lot 10H

    The exhibit hours are:

  • Thurs. Sept 14 from 9:30 to 3:30
  • Fri. Sept 15 from 9:30 to 2:30
  • Please come drop by and say hello!

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    How to check the orientation of a ligated insert using MacVector’s Restriction Digest and Agarose Gel tools.

    How to check the orientation of a ligated insert using MacVector’s Restriction Digest and Agarose Gel tools.

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    Annotating a gene in MacVector

    Creating biologically accurate AND beautiful maps of your plasmids is easy in MacVector. All you need to do is select some sequence, then open the FEATURES EDITOR. Every annotation is fully compatible with the Genbank specification and Feature Table.

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    Downloading hits from the MacVector 15.5 BLAST Map results tab

    The MacVector 15.5 BLAST Map results tab is a unique interface for examining the annotations around hits to a query sequence. Each pane in the display represents a High Scoring Segment Pair, as seen in the BLAST Aligned Sequence tab. At the lower left corner of each pane is a Download button – when you click on it, a popup menu appears with several options.

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    The major options are to either download the entire genome, remembering this might be many Mbp in size, or to just download the displayed fragment. In general, MacVector displays the High Scoring Segment Pair region of the sequence, plus 2kb on either side to provide context, and that is what will be downloaded. To reduce the number of mouse-clicks when scrolling through a lot of results, Download to Last Folder places the downloaded sequence in the last folder that you selected (or your Downloads folder if you’ve never selected one before).

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    Controlling Automatic ORF Display

    MacVector 15.5 automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab.

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    The setting for this are controlled by the MacVector | Preferences | DNA Map pane, along with the automatic Show restriction sites settings.

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    The Minimum Number of Codons setting is fairly obvious. 5’ ends are starts and 3’ ends are stops are used for linear sequences and will display ORFs coming into the sequence that do not have a start codon, or ORFs that read out of the sequence without a stop codon. Codons after stops are starts is useful if you just want to know the locations of the longest possible ORFs in a sequence, irrespective of the existence of a start codon. Finally, the Suppress annotated CDS ORFs check box prevents the display of ORFs that are already annotated. However, if a potentially longer ORF is present, e.g. there is another ATG codon upstream, that ORF will be displayed. You can read more details here.

    The appearance of the ORFs can be controlled using the Options | Default Symbols menu item.

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    Use the BLAST Map to better identify blast hits

    With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication of what features are present on the database sequence at the alignment location. MacVector 15.5 has a unique BLAST Map result tab that shows the actual annotations around the alignment location for each high scoring segment pair.

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    If a sequence is highly annotated, such that not all of the features are visible, simply holding the mouse over the appropriate pane will expand the pane to display all of the features. If you have already annotated (or partially annotated) your query sequence, those features will appear in the grey background “overlay” pane – that stays locked to the top of the window while the hits can be scrolled underneath it.

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    Generating a primer report to send to your Oligo Synthesis service

    QuickTest Primer is a great tool for primer design. Paired with Primer Design/Test (Pairs) it gives you great control and flexibility for designing primers with tails, mismatches, silent mutations, one out sites and more.

    Once you’ve designed your primer the next step is to get it synthesized. QuickTest Primer will produce a PDF report of your primer with a single click on the Report button. The report contains all the information you need about your primer, including sequence, any mismatches between the primer and template, any restriction sites you have created, the melting temperature of the oligo, molecular mass, %GC and much more. Great for sticking in your lab book or emailing to the oligo synthesis service.

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    How to toggle between 1 and 3 letter amino acid codes

    MacVector displays amino acid translations in many different result windows. You can drill down to the residue level in the Map tab and see translations of CDS and other translatable features and see translations in the plain text views and the Quicktest Primer interface. The translations can be viewed as either single letter codes or as triple letter codes. This is controlled by the Preferences | Text View pane. Simply toggle this and click on the Apply button and all of the open views will update with the new setting.

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