Print Agarose Gel images with black bands on a white background

By Chris | Published: June 6, 2016

The new simulated agarose gel function in MacVector 14.5 creates photorealistic agarose gels that look just like the real thing. However, if you want to print a record of a gel on a laser printer, the standard white bands on a grey background are not always ideal, if for no other reason than it uses a lot of toner! One great way around this is to simply view the gel in “Black on White” mode. You can adjust this by clicking on the Prefs button on the Gel window toolbar.

With the Gel Color Mode set to Black on White the image becomes inverted and you can print to a laser printer so you have a permanent record of the Gel without wasting toner.

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Creating cloning construction flowcharts in third party applications

By Chris | Published: June 6, 2016

We’ve previously discussed how every ligation is documented. You get a Frag annotation that contains the date, source sequence, enzymes used and any end modification that was done to that fragment during the ligation.

However, we had regular requests to make it easier for users to document their constructs in other ways. For example, being able to construct a flow chart showing how a construct was made for your lab book.

So in MacVector 14.5 we added PDF export to the Cloning Clipboard. Now you can copy and paste a digested fragment directly into a graphical application, such as Adobe Illustrator. This makes it easy to create a flowchart of a cloning strategy.

  • Select the fragment in the Cloning Clipboard.
  • Use EDIT > COPY
  • Move to your application and use EDIT > PASTE

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    The fragment is copied, exactly as it is displayed in the Cloning Clipboard showing restriction enzymes that have been used to digest it. All fragments are copied as linear images, so if you need to show a circular vector, then in the Map tab just copy and paste that. The fragments are copied at a fixed width size, irrespective of the actual fragment sequence length. However, if you need finer control over your fragment before creating a PDF of it, then simply double click on the fragment. It will appear in a new MacVector sequence window which you can modify before copying it as a PDF.

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    You can automatically use the Free version of MacVector if your serial number is in use

    By Chris | Published: June 1, 2016

    Starting with MacVector 14.5.1, if your serial number is in use, or if all the KeyServer licenses are in use, you will get a message like this when you start MacVector.

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    If you click on the Continue using Free version button, you still have a surprising amount of functionality. You can open, print and save (in any format) most MacVector document types and edit sequences, alignments and graphics. You can even perform simple “click cloning” manipulations via copy and paste of restriction fragments. Even the internet BLAST and Entrez functions are available. Granted the Analyze functions are not enabled and you will get an appropriate message if you try to use them, but MacVector will not quit.

    Prior to MacVector 14.5.1, this functionality was available, but a little less obvious.

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    With earlier versions (13.0 through 14.5.0), if you click on the Change License button, MacVector’s Preferences dialog will open, set to the Licenses tab. However, if you simply close that dialog, you can continue to use MacVector in Free mode.

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    Clearing the history in the Primer and Find dialogs

    By Chris | Published: June 1, 2016

    Many tools in MacVector store a history of sequences, or search terms, that you have previously used. For example, the Find dialog and Primer Design tools. This is accessed using a drop down menu to the right of the box where you would normally type, or paste, your sequence. This is to allow easy access to previously used sequences. This is quite useful when you are searching with the same primer over many sequences in the same session (although consider using the Primer Database for more permanent access to the same primer sequences).

    However, sometimes you may want to wipe these and start afresh. Especially if you’ve mistyped a primer sequence, and keep forgetting not to use it!

    All you need to do is right click, or CTRL click on the dropdown menu and you’ll access a menu that allows you to remove an entry or clear the history entirely. In the primer tools don’t confuse this with the drop down menu to access the primer database.

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    Controlling the realism of Agarose Gels

    By Chris | Published: June 1, 2016

    The default settings for the agarose gel display in MacVector generate a reasonable photorealistic simulation of an agarose gel. We have actually boosted the intensity of small bands quite significantly, and reduced their diffusion so that smaller bands show up a little more obviously and crisply than they might in real life. Even so, you may want to adjust the realism if you are trying to visualize small fragments. The simplest way to do this is to click on the Display toolbar button and select “Schematic” from the drop down menu. This will show all of the bands as simple lines at the same intensity. With this, you can be sure that every band is displayed, but many bands that are visible in the MacVector gel may not be visible in your actual gel.

    To have finer control over the gel appearance, click on the Prefs button. There is a section of the Preferences dialog (“Gel Simulation Realism”) that is devoted to controlling the realism of the simulation. Try changing those and clicking on the Apply button until you get a simulation you are happy with.

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    A few tips on working with digested fragments in the Cloning Clipboard

    By Chris | Published: June 1, 2016

    The Cloning Clipboard is an easy, and flexible, way to design and document your cloning strategies. Here’s two tips on manipulating a single fragment.

  • If you drag a fragment from the Cloning Clipboard to a vector, then you’ll get the ligate dialog. However, if you have already selected a pair of enzyme sites, then the ligation dialog does not appear. Instead, your fragment is immediately ligated into those two sites. This also happens if there is an unambiguous way the two fragments would ligate together. For example, an EcoRI-BamHI fragment would ligate directly into a vector digested with EcoRI and BamHI. Whereas if you’d just digest with EcoRI it would not.
  • If you need to manipulate, or save, a fragment before ligating it, then just double click on the fragment in the Cloning Clipboard. A new sequence window containing your fragment with its annotation will appear. Do remember though that the “digested end” information will be lost and in any ligation the new sequence will be treated as a blunt ended fragment

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    Changing the sequence alignment match and mismatch characters

    By Chris | Published: May 23, 2016

    Many MacVector analysis functions (e.g. Align To Folder, Create Dotplot and Internet Blast Search) display alignments where there is (by default) a vertical “|” character indicating a match between the query and database sequences. While this is very useful for identifying matching residues, sometimes you might be more interested in those residues that do NOT match. You can easily change the characters used from the MacVector > Preferences > Aligned Sequence tab;

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    In this example, I’ve changed the match character (“+1 or greater”) to a and the mismatch character (“-1 or less”) to a hash (“#”) symbol. When you click Apply, any open text alignment windows will update to display the new characters;

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    There are more details on this functionality in our 101 Tips series.

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    Visualizing ORF analysis results in the MAP tab

    By Chris | Published: May 23, 2016

    The Map tab is a powerful way to visualize and interact with your sequences. You can design primers, ligate and digest fragments from the Cloning Clipboard, visualise translated CDS regions and much more.

    The Map tab of a Results window is just as flexible as the Map tab of the main sequence window. You can Zoom to Residue to see your sequence results at the sequence level, or Drag to Zoom to show just a small region.

    A useful way to visualize an ORF analysis is via the Map tab, except zoomed to the sequence level, rather than using it as a graphical overview. When you initially run ANALYZE > OPEN READING FRAMES.. the Map tab in the results window shows the entire sequence, with graphical symbols representing ORFs. However, if you click ZOOM TO RESIDUE in the Graphics Palette, then instead you will see your sequence, any annotated features, and the amino acid sequence of any ORFs in your sequence.

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    You can also directly analyze the results within the Map tab. Just click on an ORF and copy that sequence to a new one, or do a Blast search directly on that sequence to see if it’s the coding region you are looking for.

  • Run ANALYZE > OPEN READING FRAMES…
  • Choose the appropriate settings and click OK
  • Switch to the Map tab in the Results window
  • Click Zoom to Residue in the Graphics Palette
  • Select the appropriate ORF
  • You can either copy it and use FILE > NEW FROM CLIPBOARD to create a new sequence, or DATABASE > BLAST to search for it.
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    Use File -> New From Clipboard to create new sequence documents

    By Chris | Published: May 23, 2016

    Whenever you have information copied to the clipboard, you can choose File | New From Clipboard and MacVector will interpret any data on the clipboard and create a new document of the appropriate type. While this is most commonly used for DNA and Protein sequence documents, this also works for multiple sequence alignments and data from restriction enzyme, primer and subsequence files.

    The function is particularly useful if you are using a web browser and stumble on a sequence that you would like to open in MacVector. Most web sites (e.g. Entrez and various genome browsers) have an option to view the sequence in GenBank format;

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    The trick here is to select from immediately before the LOCUS text at the very beginning of the sequence and include everything up to and including the two // at the end of the sequence. Copy that text and then File | New From Clipboard will not only create a new document with the sequence residues, but will also include all of the features and annotations. This also works with EMBL formatted sequence text and also simpler formats such as fasta, although in those cases no features are present in the data.

    Note that File | New From Clipboard has far more functionality than simply being a shortcut to File | New followed by Edit | Paste. Firstly, it automatically accounts for the type of the data on the clipboard and creates the appropriate document. Secondly, for sequence data, it can parse out any feature information contained in formatted text on the clipboard – a straight-forward Edit | Paste will handle feature data copied from MacVector sequence windows, but not from external formatted text.

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    Designing and documenting cloning strategies

    By Chris | Published: May 23, 2016

    Designing cloning strategies is easy with the Cloning Clipboard. You can perform quite complex ligations by simply dragging compatible ends together. However, when you open this construct a year later, you don’t want to have to look back in your lab book to know how you generated it. Neither do you need to!

    MacVector fully documents the cloning strategy that you used. Every single ligation is documented as a FRAG feature which is annotated to the target sequence. This is regardless of whether you used COPY | PASTE for a single fragment, or whether you ligated multiple fragments on the Cloning Clipboard and ligated that fragment into a cloning vector.

    As well as the source of the fragment and timestamp, the enzymes used to digest the fragment, and any modification of the overhang are also recorded. So if you Klenow treat a fragment to remove an overhang, that would be documented in the FRAG feature for that fragment.

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    All FRAG features from previous ligations are preserved in new ligations. So if you joined three fragments together on the Cloning Clipboard, then ligated those fused fragments into a vector you would have four FRAG features documenting exactly what you did.

    By default FRAG features are hidden, but you can easily make them visible to visualise the history of a construct by selecting the FRAG feature in the Graphics Palette and making them visible.

    Read more about documenting cloning workflows.

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