How to display and manipulate segmented Features

By Chris | Published: March 21, 2016

If you work with eukaryotic genomic sequences, you will likely have encountered coding (CDS) features that are split into multiple segments, with each segment representing a translated exon of the encoded gene. MacVector is very much aware of segmented features and ensures that all in-place translations (e.g. in the main sequence Editor with CDS translations turned on, or in the various text-based sequence displays) correctly handle segment splits within codons. In the Map tab, by default you should see segmented features drawn with lines between the “exons” as shown in this image of the cystic fibrosis transmembrane regulator gene.

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If you do not see these lines, then double-click on one of the exons to open the Symbol Editor, then change the Symbol Type to “Segmented Hollow Arrow”.

MacVector has a large number of functions related to creating and manipulating segmented features. For a more in-depth look at this, please check out this blog post.

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How to toggle between 1 and 3 letter amino acid codes

By Chris | Published: March 15, 2016

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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Viewing raw chromatogram data from .ab1 files

By Chris | Published: March 15, 2016

If you are interested in looking for or evaluating mixtures of residues in .ab1 or .scf chromatogram files, it is important to be able to extract the raw data from the four traces. You can open .ab1 and .scf files directly in MacVector by using the File | Open menu item or by dragging files onto the MacVector application icon. You *may* also be able to open files in MacVector by double-clicking on them, depending on which other applications you have installed on your machine. Once open, you can click on the Raw Data tab to view the trace data in tabular form;

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The “Tot. Area” column lists the total signal for each of the four traces combined at each peak position. The values are simply the signal units output by the sequencing machine. This is followed by the individual signal for each of the four traces (i.e. the “area under the curve”), along with the percentage of the total signal represented by that trace. So in the middle of a clean sequencing run, you might expect each base-called peak to represent >90% of the signal. Conversely, a SNP allele in a direct genomic sequencing run might show as an equal 50% mix of the two traces. The “mix” columns alert you to these possible mixed residues at different percentage levels. For example if you see “GT” in the 35% mix column, that indicates that both G and T represented more than 35% of the signal at that particular peak.

Finally, the entire list is displayed as tab separated values. This means that you can select the data and copy it into Microsoft Excel and each value will be placed into a separate cell so that you can perform additional statistical analysis outside of MacVector.

For more information, check out our 101 tips blog post.

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The easiest way to get graphics out of MacVector

By Chris | Published: March 15, 2016

You can use MacVector to create beautiful graphical representations of sequences with control over colors, patterns, fonts, symbols and many other aspects of the layout. The easiest way to get the graphics into another application is to simply choose Edit | Copy, switch to the target application and then choose Edit | Paste. The graphics will be transferred with full vector drawing capability so that you can increase the image size while still retaining high resolution. One particularly useful application for this purpose is Preview, found on all Macintosh computers in the /Applications/Utilities/ folder. With Preview, you can choose File | New From Clipboard to create a new document containing the copied graphics;

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From here you can choose File | Export to save the graphics in a number of different file formats.

One alternative approach if using MacVector 13.5 or later is to choose File | Export Tab Contents As… This will let you directly save the graphics in a few different built-in formats.

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How to import annotated GenBank sequences via copy and paste

By Chris | Published: March 15, 2016

While MacVector does have a built-in Entrez browser (Database > Internet Entrez Search) you can easily import GenBank formatted text into MacVector via a simple copy and paste approach. Many sequence-oriented web sites have the option of viewing sequences in GenBank format. This format always starts with the text LOCUS and finishes with two forward slashes (//). Simply select starting at LOCUS, hold down the [shift] key and scroll down the document until you see the // at the end and complete the selection to that point as shown below. Choose Edit > Copy to copy the entire text. Now switch to MacVector and choose File > New From Clipboard. This will create a new window containing the fully annotated sequence.

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Restriction enzyme sites and tooltips

By Chris | Published: March 15, 2016

Quickly viewing the recognition sequence and cut site of a restriction site is very easy in the Map tab.

If you hover your mouse over a restriction site in the Map tab, a tooltip will show you the restriction enzyme recognition site, the location of the cut site, and number of times that enzyme cuts your sequence.

  • Make sure Preferences | Map View | Automatic RE Analysis is turned on

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    You can also see the full sequence and cut site when zoomed to sequence level in the Map tab.

  • In the Graphics Palette click the Zoom to Residue button.

    • See this post for further details:

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    MacVector for Windows: update.

    By Chris | Published: March 8, 2016

    It’s quite a few months since the last update on the development of MacVector for Windows.

    Work is progressing very well and a lot of the underlying functionality is now finished. The Cloning Clipboard, Restriction Enzyme analysis and QuickTest Primer tools are all done.

    The release is still some time away, but if you are excited as we are to see MacVector reach Windows, then we’re getting a lot closer!

    Features Editor

    MV4Win FeaturesEditor

    Primer Design

    MV4Win QT Primer

    Restriction Enzyme Analysis

    MV4Win RE

    Cloning Clipboard

    MV4Win Cloning

    MacVector for Windows will not be a Java version of MacVector, nor is it a carbon copy of MacVector (for Mac!). MacVector, the original, is designed for, and fully integrates with the OS X environment. We like to say that if you can use a Mac, you can analyze your sequences with MacVector. MacVector for Windows is the same. A truly native application that is easy to use for anybody familiar with Windows.

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    How to reset the numbering after pasting a DNA fragment

    By Chris | Published: March 7, 2016

    When you copy a section from a long sequence and paste it into a new MacVector window, the original numbering from the original sequence is retained. This is very useful if you want to work on a shorter segment of a genome without losing the original numbering. However, sometimes it is preferable to have the numbering start at “1”. Its simple to do that in MacVector: just right-click in the Editor tab of the sequence window ([control]-click if you have a single button mouse or trackpad) and choose Reset Origin to 1 from the popup menu.

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    How to remove gaps from a sequence

    By Chris | Published: March 7, 2016

    There are often times when you end up with a sequence containing gaps, especially if you make extensive use of the Align To Reference, Contig Assembly or Multiple Sequence Alignment interfaces to generate consensus sequences. You can select and copy the consensus sequence, or even individual aligned reads, from the Align To Reference and Contig editor tabs. The copied sequence can then be pasted into a sequence editor window, or a new document can be created by choosing File | New From Clipboard. In either case, if any gaps were present in the copied sequence, these will be preserved when pasted. MacVector does this because there are times when you might want those gaps preserved and, as you will see, it is a lot easier to remove them after the paste than it would be to type them back in by hand!

    For MacVector 14.5 we introduced a new REMOVE GAPS function where all you need to do is select the sequence and run it. Edit | Select All then run Edit | Remove Gaps. This tool works on all sequences, for example in the Align to Reference and MSA editor, and single sequences.

    For MacVector 14 and earlier you will need to search for gap characters and then remove them using the Edit | Find | Find… menu item. The key to this functionality is that you must first check the Literal box before you can add a gap character in the Find box;

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    Just leave the Replace box empty, then when you click on the Replace All button, all of the gaps will be deleted. Note that if the Replace All button is inactive, that usually means that no gaps are actually present in your sequence.

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    How to automatically annotate bare sequences

    By Chris | Published: March 7, 2016

    If you have an unannotated vector or other sequence that you’ve been sent from a sequencing lab, downloaded from a web page or been sent by a colleague, it can be very tedious to manually create all the features that you believe are present on the sequence – assuming you even know what is supposed to be there! Luckily, there is a simple solution in MacVector: Open the sequence (or create a new Nucleic Acid Sequence document and paste in the residues), make sure you have the Topology set correctly to either circular or linear, then choose Database | Auto-annotate Sequence.

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    The main key to this functionality is to select a suitable Sequence Folder to scan, as circled in the screenshot. A good place to start when trying this out for the first time is the /Applications/MacVector/Common Vectors/ folder. We have collected a selection of common vectors from a variety of manufacturers, made sure they are correctly annotated and given each feature a unique and attractive graphical appearance.

    After clicking OK, MacVector will scan through the entire hierarchy of folders in Common Vectors, opening each sequence, extracting the features and determining, via sequence similarity, if the same feature is present in your starting sequence. When complete, a dialog will appear listing the number of features analyzed and how many were found on your sequence. MacVector is clever enough to know not to count duplicate features, and also to allow a little “fuzziness” in the similarity calculation.

    Of course, this will only find features common to these cloning vectors – repeat the search with a folder full of your own annotated sequences to find those. Then, if there are still features missing, manually add those. This way, you can slowly build up your own collection of curated sequences to act as a “database” for rapid annotation of any new sequences you acquire.

    There is a longer blog post and a tutorial installed on your computer at:

    /Applications/MacVector/Documentation/Auto Annotation Tutorial.pdf

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