Tear-off Result Window Tabs: make viewing results easier.

By Chris | Published: July 14, 2017

All analysis results for an individual sequence are collected into a single tabbed result window to reduce window clutter. However, there are times when it is very convenient to have results displayed in side-by-side windows. For example, if you run a dot plot you can zoom in to view sections of the comparison by drag-selecting over a region of interest in the Matrix Plot tab and the Aligned Sequence tab will update to only display the text alignments across the new selection. Constantly toggling between the tabs to drill down to the region you are interested in (e.g. a potential splice site on a genome versus cDNA alignment) can be very frustrating.

All you need to do is to click on the title of a tab, hold down the mouse button, then drag the selected tab away from the parent window. When you let go of the mouse button, a new window will be created containing just that single tab.

NewImageNot only that, you can organize the tabs into multiple windows if you like. If you drag a tab from one window and drop it onto the tab bar of another window (this only works on the tab bar, you can’t drop on the content region of a window), then the tab will be added to the target window.

Give it a try and get your result windows under control!

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MacVector 15.5.3

By Chris | Published: July 10, 2017

There’s another update available with a few minor bug fixes. Update by going to MACVECTOR > CHECK FOR UPDATES

The changes in MacVector 15.5.3 are described in the Release Notes . You can also read more about the new features in MacVector 15.5 on our What’s New In MacVector 15.5 page.

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MacVector for Windows update: Using the Cloning Clipboard.

By admin | Published: June 19, 2017

Macvector for Windows is getting closer.

Here’s a short screencast on using the Cloning Clipboard:

 

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Use the Edit | Transformations menu to change the case of sequence residues

By Chris | Published: June 7, 2017

Sometimes it is useful to use a mixture of cases in a sequence. You might want to flag an interesting region and have it easily identifiable in other views. You can change the case of a selected region of a sequence in MacVector using the Edit | Transformations menu.

The case is maintained in all of the related MacVector sequence display windows. In particular, the plain text output windows from all of the analysis functions honor upper/lower case so you can easily identify results surrounding your region of interest.

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Using BLAST to automatically annotate a sequence

By Chris | Published: June 7, 2017

You can use the Database->Auto-Annotate Sequence function to quickly annotate a bare sequence using existing annotated sequences on your file system. However, this only works if your collection of sequences contains features representing all parts of the bare sequence. Luckily, if you have an unannotated region after running Auto-Annotate, you can use MacVector’s built-in BLAST function to find and download matching annotated sequences, then run Auto-Annotate to add features to the blank region.

If you are interested in this, the full steps are discussed in this blog article.

  • Briefly, the first step is to select the unannotated region of your test sequence. You can do this in the Map tab by choosing the sequence selection mode in the floating graphics palette and drag-selecting the blank region.
  • Choose Database->Online Search for Similar Sequences (BLAST) to find the best hits to the blank region.
  • Select the top four or five hits in the BLAST Results Description List and choose Database->Retrieve To Folder.
    Now run Database->Auto-Annotate Sequence, choosing the folder where you retrieved the matching hits.

    • NewImage

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    The MacVector Team are at the ASM2017 in New Orleans (2-5 June).

    By Chris | Published: May 23, 2017

    We’re at ASM Microbe 2017 in New Orleans from Friday until Sunday (2-5 June).

    The exhibit hall hours are a more respectable 11:30 or 12 until 18:00 now (last year was a quite early 7:30 until the afternoon).

    We’re on booth #2247.

    Please do drop by. We’ll be showing our latest release, MacVector 15.5 and giving tips on getting the most out of it. So whether you are an experienced user, or have never used MacVector, then please drop by and say hello!

    We’ll also be showing our upcoming “MacVector for Windows” release. So if you’ve been waiting patiently for this, come have a look!

    See you in New Orleans!

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    Use the BLAST Map to better identify blast hits

    By Chris | Published: May 16, 2017

    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 new unique BLAST Map result tab that shows the actual annotations around the alignment location for each high scoring segment pair.

    NewImage

    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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    Controlling The Automatic ORF Display in MacVector 15.5

    By Chris | Published: May 16, 2017

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

    AutoORFExample

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

    DNA Map Prefs

    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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    MacVector 15.5 is out: Graphical BLAST and automatic ORF display.

    By Chris | Published: May 10, 2017

    Our latest release, MacVector 15.5, introduces an entirely new way to view the results of BLAST searches, with an interactive graphical interface that let’s you easily visualize where your query maps to a hit. Unannotated Open Reading Frames are now automatically displayed whenever you open a DNA sequence. A number of changes to the Align To Reference and Contig Editors simplify the task of closing gaps and resolving repeats in sequencing assemblies.

    BLAST MapResults

    Graphical BLAST Results

    Displays a fully annotated alignments of your query sequence against each high scoring hit. Genes and other features are displayed for both query and hits. This allows you to clearly see which genes your query is mapped to. For each hit, you can also just download the alignment only. Very useful when your query is a single gene, but hits are genomes or chromosomes.

    ORF AutoAnnotate

    Automatic ORF Display

    MacVector now automatically searches for open reading frames in every DNA sequence that you open. You can quickly annotate the ORF to your sequence with a right mouse click.

    Align to Reference

    Many new tools have been added for closing gaps, and resolving repeats, in sequencing assemblies.

    Misc changes

    A variety of menu changes will make many tools more accessible to less experienced users. A number of optimizations have been made to better handle opening an analyzing extremely large sequences and reference alignments.

    How to update to MacVector 15.5

    If you have active maintenance and are running MacVector 13.0.1 or later then you should have been notified about the new release already. At that point you have the option to automatically upgrade to MacVector 15.5. To install this version, you must have a maintenance contract that was active on 1st February, 2017. You must also be running OS X 10.7 or later.

    If you have an older version of MacVector then download the trial and request an upgrade quote.

    If have downloaded the trial in the past then downloading a new trial will give you a fresh 21 days to evaluate MacVector even if a previous trial license had expired.

    Remember that when a trial expires it becomes MacVector Free.
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    Clone construction using Digest/Ligate rather than Copy/Paste

    By Chris | Published: April 24, 2017

    In previous post we looked at using Edit | Copy and Edit | Paste to quickly and simply create new constructs using Restriction Enzyme sites. This post will look at an alternative approach, using the Digest and Ligate buttons and the Cloning Clipboard.

    The sequence window Map tab has two buttons called Digest and Ligate. These work in a very similar manner to Copy and Paste. If you select a restriction fragment, Digest becomes active.

    NewImage

    The difference between Digest and Copy is that instead of copying the fragment to the global system pasteboard, Digest copies it to MacVector’s internal Cloning Clipboard.

    NewImage

    The Cloning Clipboard keeps a history of every fragment you have Digest’ed, though it’s easy to remove individual fragments or reset the entire clipboard.

    The Ligate button is very similar to invoking Paste, except that instead of pasting the contents of the global system clipboard, it pastes the selected fragment on the Cloning Clipboard. Again, if the ends are not compatible, a dialog will be displayed letting you fill or cut back the ends to force a blunt ended ligation.

    You can also join fragments together on the Cloning Clipboard by simply clicking in the circles at the end of fragments, then dragging and dropping those onto a different end.

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