In this part of the tutorial, you will translate the output sequence from Part B and save the results as a second output file.

  1. Click the Templates tab on the right of the SeqNinja window and choose Translate. A new project tab opens with the template loaded.
  1. Click the Choose Sequence(s) button and navigate to the file Extracted genes.fasta.
  1. From the Translation Table drop-down menu, choose NCBI: 11. Leave the Reading Frame drop-down menu at the default setting.
  1. To the right of the Save Results As button, type the name Translated genes. From the Format drop-down menu, choose Fasta. The output file will automatically be saved in the working directory specified earlier.

The script now appears as follows:

  1. Run the script by clicking the Run tool (). When the run finishes, the Run Completed dialog will appear. Click on the link to open the tutorial data folder.
  1. To view the translation results, open Translated genes.fasta in DNASTAR’s Protean 3D or in any text editor. The table below shows the extracted and translated genes from the three files.
Filename Extracted and translated genes
LAMCG.seq int
pbr322.seq tet
tethis21.seq (none found)

As you can see from the table, there were no annotated genes in the tethis21.seq file. However, all three files do have annotated CDS features. To extract and translate these:

  1. Go back to the SeqNinja project tab that contains the extraction step and select CDS from the Features drop-down menu . Click Run again and overwrite the previous result file.
  1. Click on the SeqNinja project tab with the translation step and click Run. Overwrite the previous files. Open the results in a text editor and see how they differ from those in Step 6.

Proceed to Part D: Extracting and translating features using an alternative method.

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