*Note: To create a new project and add sequences in their original formats, see the topic Create a new project.
MegAlign Pro 17.6, released in 2024, can automatically translate selected nucleotide sequences (or subranges of those sequences) and add them to a new project tab. These sequences can then be aligned using protein-optimized alignment settings.
Two reasons you may want to utilize this feature are if:
- You want to apply customization options in the alignment algorithm that are only available for protein sequences. For example, if you choose Align with Options and select Clustal W, there are different customizable settings for nucleotide and protein sequences.
- You want to align a group of related sequences that consist of a mixture of DNA and protein sequences. This method lets you automatically translate the DNA sequences and add them to a new project. You can then add the sequences that were already in protein format to that project and align all of the sequences as a group.
*Note: If the organism whose sequences are loaded into the MegAlign Pro project uses a non-standard translation code, be sure to select if from the
Sequences > Genetic Code submenu before following the steps described below.
| Task |
How to |
| Populate a project with the translations of nucleotide sequences from a folder |
- Create a new project if an appropriate one is not already open.
- If the organism uses a non-standard genetic code for translation, select the code from the Sequences > Genetic Code submenu.
- Choose File > Add Sequences Translated.
- Select the files containing sequences you would like to use in translated form. Then press Open.
|
| Create a new project containing translations of the currently selected nucleotide sequences |
- From any graphical view, select the sequences you would like to use (in translated form) in the new project.
- Do either of the following:
- Click the Translate selection in a new alignment project tool (
![]() ) in the top left section of the MegAlign Pro window.
- Choose File > New Alignment Project > With Selected Sequences Translated.
These options are disabled unless one or more sequences have been selected.
|
| Create a new project containing translations of the currently selected nucleotide subsequences |
- From the Sequences view, select the subrange you would like to translate and add to the new project. For instance, you could click on a single feature; only that feature in that one sequence would be translated and added to the new project. By contrast, triple-clicking on the feature would select that feature in all sequences, and all of that data would be translated and added to the new project. To learn about various options for selecting a subrange of one or more sequences, see Make a Selection.
We recommend using the Translation track for guidance to ensure your selection is complete and in the correct frame. Multiple sequence alignment algorithms don’t consider CDS boundaries. Therefore, when you triple-click on a CDS to select a subsequence, the selection might include residues that shift the translation frame. MegAlign Pro provides several ways to address this. See Edit gaps in a sequence for more information.
- Use the menu command File > New Alignment Project > With Selected Subsequences Translated. This option is disabled until you have made a selection.
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) in the top left section of the MegAlign Pro window.