Trial download and updating issues!

By Chris | Published: May 20, 2016

Over the past few weeks we’ve had a few reports of trial downloaders having problems installing the trial. We also had a few calls from users with problems updating to the latest release of MacVector 14.5 (14.5.3).

The problem manifests itself by showing an error message that the file is “damaged” and cannot be installed.

We’ve got to admit that at first we were stumped. We could not see the problem ourselves and we could not identify a common theme to users with problems. However, one of our clever developers finally tracked this down to a bug in OS X 10.11 that caused problems with signing the release.

Starting with OS X 10.7 Lion, Apple increased the security measures for installing and running applications using a technology called GateKeeper. The default settings for OS X only allows applications from either the App Store or from registered developers to run. MacVector, Inc. is a registered developer and the MacVector application is signed to say so that it has not been modified or tampered with in any way.

This recent problem was caused when we signed the application on OS X 10.11 El Capitan, but the application is then installed on OS X 10.7 to 10.10. We thoroughly test every new release of MacVector, no matter how minor the release is. However, due to the sporadic nature of this issue we completely missed this one! Sorry!

Apple announced that they fixed that bug in OS X 10.11.5, which was released a few days ago. We’ve rebuilt and signed MacVector using the new OS and our testing so far shows that this has fixed the issue.

If you’ve downloaded the trial in the past few weeks and been unable to install it, then please let us know and we’ll give you a new 21 day license and a link to download it.

If you’ve had problems updating MacVector, then just run MACVECTOR > CHECK FOR UPDATES… again and it will now be installed correctly. Alternatively download the full installer. It’s a good idea to do that now and again anyway as all the ancillary files (e.g. Restriction enzyme files etc.) will also get updated.

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Calculating the PCR annealing temperature for a pair of primers

By Chris | Published: May 15, 2016

MacVector not only calculates the melting temperature (Tm) for any primers you design, but also displays the recommended annealing temperature (Ta) that you should use in PCR experiments using those primers. You can access the main MacVector interface for designing pairs of primers using Analyze | Primer Design (Primer3). From here you can ask MacVector to search for suitable primers using the popular Primer3 algorithm, or simply test a pair of existing primers for suitability. In either case, one of the output options is a Primer3 Spreadsheet tab.

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Here the Tm of the Left and Right primers is displayed, along with the Tm of the product. The far right column also displays the recommended Ta for that primer pair. For more details on how this is calculated, please check out a recent blog post on the subject.

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Use dot plots to quickly confirm similarity between two sequences

By Chris | Published: May 15, 2016

We occasionally get e-mails from users who think that two sequences should align using ClustalW or the Align To Reference function, but the algorithms cannot find any meaningful matches. In these cases, the first thing I do is open both sequences and then create a dot-plot between them using the Analyze | Create Dotplot | Pustell DNA Matrix function. There is also a protein version and even a DNA versus Protein version. This is a great tool for getting a quick overview of the sequence similarity between a pair of sequences.

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A – The two sequences are essentially identical and in the same orientation. The diagonal runs from top left to bottom right and is drawn in black. You also see this pattern if you test a sequence against itself.

B – The two sequences are essentially identical, but one is “flipped” relative to the other so you see a full-length diagonal running bottom left to top right in blue.

C – One of the sequences has a section in the middle that is inverted relative to the other.

D – The two sequences are similar, but are far from identical, resulting in a dotted line.

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Downloading BLAST Hits from the NCBI direct to your desktop

By Chris | Published: May 15, 2016

When you use MacVector to run a BLAST search, did you know that you can download any matching sequences directly from the BLAST Description List window? Simply select text on any part of the line(s) representing the sequence you want to download and choose Database | Retrieve To Desktop or Database | Retrieve To Disk to download the selected sequences.

Retrieve To Desktop will download and open each selected sequence in a window on your desktop. Retrieve To Disk will prompt you for a location on your hard drive – the better option if you want to download more than just a few sequences.

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Troubleshooting problems with MacVector

By Chris | Published: May 15, 2016

MacVector generally just works. However, it’s a very rare piece of software that does not have occasional technical faults. Every now and again we do get reports to MacVector Support about such technical issues. Whenever we come across such issues we document them and also try to fix it so they never happen again in one of our regular minor updates.

One of the most common support calls we get is from users with old versions of MacVector trying to install on a new Mac they’ve just got. “I get a -5000 error when I try to activate my license” or “I’m getting an error that the license cannot be saved, unable to write license to disk”. It’s an easy fix, but upgrading works too as the problem was solved quite a few versions back. .…and there’s many, many new tools and features in the last few versions! If you think you are entitled to a newer version than the one you have installed, then email MacVector Support and ask what version your license is valid for.

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Save trace files as images

By Chris | Published: May 10, 2016

You can open ABI chromatogram (“Trace”) files directly in MacVector and analyze them like any other sequence. You can also use them in the Align To Reference and Assembler interfaces, where the actual trace data will be displayed, or in any other function that accepts external sequence files.

Sometimes you just want to print out, or create an image of, the trace data so that you have a permanent record of the chromatogram – perhaps because it has an important base change or a mixed residue. The easiest way to do this is to simply choose File | Print, then click on the PDF button in the print dialog and choose Save As PDF... MacVector will output the entire chromatogram, taking the current height and scaling of the Editor tab as its guide. To have more control over this, click on the Fit To toolbar button and select the number of “rows” you would like to see on a page. Or choose Fit On Single Page to get the entire chromatogram printed on one page. Note that in versions of MacVector prior to 13.5, the button was located in the bottom left of the Editor window, but the options are identical. If you would prefer the file in a different format, open it in Preview.app and use File | Export to save in e.g. tiff or jpg formats.

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Annotating the sequence in the Editor tab

By Chris | Published: May 10, 2016

You can very quickly annotate a region of interest in your sequence in the Editor tab. For example showing introns in lower case or highlighting CDS features with a colored background.

To enter sequences as mixed case.

  • Enable Edit | Transformations | Enable Mixed Case Entry
  • Type your sequence using SHIFT or CAPS LOCK

    • To color a region.

  • Select the region you want to highlight.
  • Choose Edit | Transformations | Color.

    • To change the case of a region.

  • Select the region you want to change to lower case
  • Choose Edit | Transformations | Make Lower Case.

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    Displaying features in the Editor tab

    By Chris | Published: May 10, 2016

    The Map tab shows a richly detailed graphical representation of your sequence. However, sometimes you just need a overview of annotation along with sequence. MacVector makes it easy to display features directly on the sequence in the Editor tab.

    Only a subset of a sequence’s features are displayed due to limited room. You can choose to display all visible features or only features that are displayed on the sequence level in the Map tab.

  • Open the MacVector | Preferences | Colors pane.
  • Switch Sequence Editor to show Color Background or Color Residues.
  • Toggle to choose between all features visible in the Map tab or Only features located on the sequence.

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    Create constructs using the Cloning Clipboard

    By Chris | Published: April 18, 2016

    You can create new constructs in MacVector by selecting two restriction enzyme sites, choosing Edit -> Copy, selecting a target restriction site in a different molecule and then choosing Edit -> Paste. It works great and fully understands compatible overhanging sticky ends preventing you from accidentally creating biologically impossible molecules. However, a far more flexible approach is to use the Cloning Clipboard. Select the restriction sites at the ends of your source molecule in the Map tab (hold down to select the second site), then click on the Digest toolbar button (or choose Edit -> Digest) and the fragment will be placed onto MacVector’s Cloning Clipboard. You can then join fragments together by simply clicking on an end and dragging it onto the end of a different fragment.

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    Again, MacVector understands that the ends need to be compatible before they can be joined and even allows you to fill or cut back ends to make them compatible. You can join one end of a single molecule to the other to create a new circular molecule, or click on the Circularize button. You can also use this approach to create complex multi-step molecules generated by Gateway or Gibson cloning technologies.

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    Using the Primer Database to store your lab’s collection of primers

    By Chris | Published: April 18, 2016

    MacVector 14 saw the introduction of the new Primer Database tool. This allows you to save and retrieve primers from the Primer Database from the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites. The tool comes with a starter database of primers, but you can use existing subsequence files or import primers from Excel.

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    To save a primer from QT Primer:

  • Open ANALYZE > QUICKTEST PRIMER
  • Design your primer
  • Click ADD TO…
  • Give the primer a name and add a comment. Click OK

    • To save a primer from Primer Design:

  • Open ANALYZE > PRIMER DESIGN (PRIMER3)
  • Design your primer pair
  • In the spreadsheet right click on a primer
  • Choose ADD PRIMER TO DATABASE
  • Give the primer a name and add a comment. Click OK

    • To use the Primer Database Search:

  • Open your sequence
  • Select ANALYZE > PRIMER DATABASE SEARCH
  • Choose parameters and click OK

    • Read more..

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