Quick shortcuts to zoom in and out in the Single Sequence Map tab

By Chris | Published: March 29, 2016

One very useful feature of the single sequence Map tab is that you can use the mouse to “drag-select” and zoom in to view a smaller section of a large sequence. Apart from the utility of using this to “drill down” to view individual genes, or even residues, in a large sequence, if you do this in the Map tab of a result window, the other associated text results will refresh to show just the results relevant to the shorter “zoomed” sequence.

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To get back to the starting position (i.e. to show the full sequence), simply Double-Click anywhere in the Map window.

There are other useful shortcut keys;

  • Up Arrow – zooms in 2-fold, centered around the middle of the currently visible segment.
  • Down Arrow – zooms out 2-fold.
  • Left Arrow – if zoomed in, nudges the zoomed region left by a few percentage points.
  • Right Arrow – if zoomed in, nudges the zoomed region right by a few percentage points.
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    Opening matching sequences from an Align To Folder search

    By Chris | Published: March 29, 2016

    You can use the Database->Align To Folder menu function in MacVector to quickly search any set of folders on your hard drive for matching sequences. Its like having your own personal BLAST search that just scans files of interest to you. The great thing is, when you find matching sequences, you can easily open them by selecting the hits and choosing Database->Retrieve To Desktop. Try this: open a sequence with a feature you are interested in, select that feature in the Map tab, then choose Database->Align To Folder. Choose a search folder containing a collection of sequences and click OK. After the search has completed (typically just a few seconds unless you are screening many thousands of sequences), switch to the Folder Description List tab which will list those sequences with the best match to your feature. Select a few rows (you don’t need an entire row to be selected), followed by Database->Retrieve To Desktop.

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    The selected sequences will now open in individual windows on your desktop. For more information on this functionality, please check out this post in our 101 tips series.

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    Smart Folders and MacVector

    By Chris | Published: March 29, 2016

    OS X’s Finder has many features for quickly finding and working with your files. Spotlight Search is one such tool that most Mac users are familiar with. However, Smart Folders is a tool that is very useful but often overlooked.

    Smart Folders allow you to create a dynamic folder whose contents are derived from a Spotlight Search. The folders are permanent but dynamically updated, and can even be shown directly in the sidebar of Finder.

    You can have very simple Smart Folders or complex ones. Smart Folders are very useful for keeping track of your MacVector sequences. For example “show me all Assembly Projects last modified within the past month” or “Show me all trace files from the past seven days“.

    To create a Smart folder to show all MacVector sequences last opened in the past month:

  • Click FILE | NEW SMART FOLDER in Finder.
  • Click “+” next to SAVE
  • Enter “KIND, is OTHER macvector” for the search terms
  • Click “+”
  • Enter LAST OPENED DATE is WITHIN LAST – 1 – MONTHS
  • Click SAVE and enter a name. Don’t forget to include it in the Sidebar.

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    There are many other useful Smart Folders you can use to help you organise your MacVector sequences.

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    Restriction enzyme sites in cloning vectors show compatible ends with fragments in the Cloning Clipboard

    By Chris | Published: March 29, 2016

    If you are looking for compatible cloning sites for a fragment, MacVector has a simple color-coded function to identify potential target sites in a vector. First select the fragment you wish to clone by clicking on two enzymes in the Map view of a single sequence document or from a restriction enzyme search result. Then choose Edit | Digest to place that fragment onto the Cloning Clipboard. Make sure that fragment remains selected on the Cloning Clipboard, then bring the Map tab of any potential vector sequence to the front. Any restriction enzyme sites that are compatible with the left hand end of the Cloning Clipboard fragment will display with a pastel red background. Restriction sites compatible with the right hand end will display with a pastel green background.

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    (Read More..)

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    Quickly checking a small sequencing project

    By Chris | Published: March 21, 2016

    For analyzing large sequencing datasets you need Assembler. However, many times you do not need a powerful tool but just a quick way to check some sequencing data. For example for checking small sequencing projects, such as a site directed mutagenesis, looking for SNPs in a PCR product, cloning a gene or checking your latest construct is correct. MacVector has a built in tool called ALIGN TO REFERENCE that’s specifically designed for such tasks.

    The tool is capable of quite complex workflows, including aligning mRNA and EST data against genomic references. However, for checking your latest construct the steps are pretty simple:

  • Open up your reference.
  • ANALYZE | ALIGN TO REFERENCE
  • In the new window click ADD SEQS and add your reads or trace files.
  • Click ALIGN and choose SEQUENCE CONFIRMATION
  • Choose the defaults and click OK.

    • The reads will be aligned against the reference and show a consensus. Reads are automatically reverse complemented if needed.

    Click on the DOTS button to hide all bases that match the consensus, and only show mismatches. There’s also the MAP tab that shows a graphical view of all reads and the reference. You can align against a circular reference too!

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    Read more..

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    Testing pairs of PCR primer

    By Chris | Published: March 21, 2016

    Over the past few releases of MacVector, we have changed primer testing considerably. Now all primer design and testing can be done using Quicktest Primer for a single primer and Primer Design (Primer3) for pairs of primers.

    If you want to test an existing pair of primers for suitability, use the following steps:

  • Open the target sequence and choose Analyze | Primers | Primer Design/Test(Pairs).
  • Click on the Use This Primer checkbox for both the left and the right primer. The mode changes to Test Primer Pair.
  • Now paste or type the primer sequences you want to test into the two edit boxes.
  • If you get warnings that the primer(s) are of an invalid size or %G+C, then click on the Advanced options button and modify the settings in the Characteristics tab.
  • Click on the OK button to run the test.

    • A window will appear showing any problems in red text.

  • Select the Spreadsheet and Graphical Map checkboxes and click OK.

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    Read more..

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    Quickly design a pair of primers to amplify a feature

    By Chris | Published: March 21, 2016

    Designing a pair of primers to amplify a single feature is pretty quick with MacVector.

  • Select a feature in the MAP tab.
  • Run Primer Design/Test(Pairs).
  • Ensure the dropdown menu is set to AMPLIFY FEATURE.
  • Click OK.
  • Check the summary shows that primers have been found and select the spreadsheet and graphical view.
  • Click OK.

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    Tear-off Result Window Tabs

    By Chris | Published: March 21, 2016

    Starting with MacVector 13 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.

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    Not 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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    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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