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!

Tag Archives: translation

Controlling Automatic ORF Display

MacVector 15.5 automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab. The setting for this are controlled by the MacVector | Preferences | DNA Map pane, along with the automatic Show restriction sites settings. The Minimum Number of Codons setting is fairly obvious. 5’ ends are […]

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How to toggle between 1 and 3 letter amino acid codes

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 […]

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Optimizing the Reverse Translation function

The Analyze | Reverse Translation menu option lets you create a DNA sequence from a Protein sequence, reverse translated using a specific Genetic Code (by default, the Universal Genetic Code). The default option creates a DNA sequence with N’s and other ambiguities reflecting the degeneracy of the genetic code. This is great if you want […]

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Displaying CDS features as translations in the Map tab.

Where appropriate, features can be shown as residues when there is sufficient space to show them (for example when zoomed to residue). By default this is enabled for certain features, e.g. CDS features, genes, but it is controlled from the Symbol Editor and can be turned on/off for most features. In the Map tab, double […]

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How to toggle between 1 and 3 letter amino acid codes

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 […]

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How to display translations in the sequence editor

For those of you who like to type in DNA sequences, or do manual editing to the sequences, it’s really useful to be able to see the translations above or below the sequence residues in the Editor tab of the single sequence window. If you are a long term user, you’ll be familiar with the […]

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101 things you (maybe) didn’t know about MacVector: #10 – Displaying Amino Acids As Triple Letter Codes In Translations

Following on from my last post about turning on translations in the sequence Editor, I thought I should point out how to display amino acid translations using the 3-letter code rather than the default single-letter code. I don’t know about you, but I have a hard time remembering that “W” is the single-letter IUPAC code […]

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101 things you (maybe) didn’t know about MacVector: #9 – Showing Translations In The DNA Sequence Editor

If you have used MacVector for many years, you’ll remember the days when the single sequence editor was THE main way you interacted with MacVector. When MacVector 10 was introduced back in 2007, the Editor became just one tab in the single sequence window along with Map, Features and Annotations tabs, all of which at […]

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MacVector 12: Annotating the sequence in the Editor View.

This is in a series of blog posts on interesting highlights of new features added to MacVector 12 In the last survey a popular request was to be able to change the case, alter the colour, or otherwise being able to annotate sequence directly in the Editor view. You’ve been able to use the Map […]

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Displaying translations alongside your DNA sequence

There’s a few ways to display an amino acid translation in the same window as your DNA or RNA sequence. (1) You can show either three or six frame translations directly in the editor. To do so simply press and hold down the STRANDS toolbar button. You’ll see the following menu and be able to […]

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