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!

MacVector for Windows update: Using the Cloning Clipboard.

Macvector for Windows is getting closer.

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

 

Posted in Development | Tagged , , | Leave a comment

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

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.

NewImage

Posted in Tips | Tagged , | Leave a comment

Using BLAST to automatically annotate a sequence

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

    Posted in Tips | Tagged , , | Leave a comment

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

    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!

    Posted in General, Meetings, Tips | Tagged , | Leave a comment

    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 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.

    Posted in Tips | Tagged , | Leave a comment

    Controlling The Automatic ORF Display in MacVector 15.5

    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.

    Posted in Tips | Tagged , , | Leave a comment

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

    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.

    Posted in Uncategorized | Tagged , , , , | Leave a comment

    Clone construction using Digest/Ligate rather than Copy/Paste

    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.

    Posted in Uncategorized | Tagged , , | Leave a comment

    Simple but accurate restriction enzyme based clone construction using Copy and Paste

    The quickest and simplest way to create restriction enzyme generated constructs in MacVector is to use Edit | Copy and Edit | Paste. The strategy to use is identical to copying a paragraph from one Microsoft Word document to insert into a second document. i.e.

  • Select the restriction enzymes flanking the source fragment in either the Map tab of the sequence window, or the Map Results tab after a Restriction Enzyme analysis. Hold down the [SHIFT] key to select the second enzyme. In circular maps, the selection always proceeds in a clockwise direction, so the order you select is important.
  • Choose Edit | Copy. This places the fragment onto the system clipboard, along with sticky end information.
  • Switch to the destination vector. Select the target restriction enzyme site(s). When selecting two sites, make sure you select the fragment you want to replace.
  • Choose Edit | Paste. If the restriction enzyme site(s) have ends compatible with the copied fragment, this will insert the fragment from the system clipboard into the vector. If the ends are incompatible, you will get a warning “ligation dialog” with options to fill or cut back ends to make them compatible.
  • NewImage

    The red line around the left ends indicates that they are compatible. If you were to fill or cut back the right hand ends you would see green lines indicating they are now compatible.

    NewImage

    MacVector will never let you create an invalid construct, so you can select/copy/paste to create new constructs safe in the knowledge that if the ends are not compatible, MacVector will always show this warning dialog.

    One final tip, if a fragment can be inserted in either orientation, hold down the [option] key and the Edit | Paste menu item will change to Edit | Paste Flipped, letting you insert the fragment in the opposite orientation.

    Posted in Uncategorized | Tagged , , | Leave a comment

    How to change the default appearance of features

    If you download a sequence from Entrez, or open a sequence that is not in MacVector format, MacVector assigns a default appearance to any features on the sequence. For example, CDS features are shown as a blue arrow with a Helvetica 9 point font label. With the advent of ultra high resolution displays, you may find that the default font is a little too small to easily view. MacVector has a Default Symbols dialog that lets you control the appearance of every default symbol. To invoke this, hold down the [option] key and choose the Options | Default Symbols… menu item. Note that if you have just started MacVector and have no open sequence windows, or if a non-sequence window is front-most, you do not need to hold down the [option] key.

    NewImage

    To change the font used for CDS features, select the Features tab, then click on the DNA CDS item in the list of feature types. Then you can click on the font button to select a preferred font using the system-wide font selection window. You can change the font for multiple features types at once by selecting multiple rows in the list using the or keys then selecting an appropriate font.

    Note that with the current version of MacVector (15.1) you will need to close and then re-open sequence files for the change to take effect.

    Posted in Uncategorized | Tagged , , | Comments closed