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!

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 select what you want to show:

EditorTranslations.png

(2) If you have CDS or exons annotated to your sequence you can display a text view that translates these features and displays them with the sequence. This is the TEXT VIEW button in the toolbar. The TEXT VIEW is highly configurable. For example you can also have each codon spaced out and aligned with its amino acid if you select “BLOCK TO PHASE”. As in the following screenshot. You may find this easier to see the frame from which the amino acid sequence is translated from.

TextView.png

If the sequence that you want to display does not have your desired translation annotated, then it is straightforward to do so.

1 – Highlight the sequence in the EDITOR

2 – Click CREATE in the toolbar to open the FEATURE EDITOR

3 – Choose CDS in the top drop down menu and choose appropriate qualifiers in the bottom section. Click OK

You can also use the ANALYZE > OPEN READING FRAMES… tool to find regions in your sequence. Once run, select the appropriate ORF in the ORF results to highlight the sequence in the editor. You can then go to step 2 above to annotate the sequence.

When MacVector 12 comes out you will also be able to see translations directly in the graphical Map view:

MacVector11MapSequenceLevel.png

Technorati Tags:

This entry was posted in General, Techniques and tagged , , . Bookmark the permalink. Both comments and trackbacks are currently closed.