Part D: Extracting and translating features using an alternative method

When translating a .gbk or .seq file that contains CDS features, the extraction step in Part B is redundant. The reason is that, during translation, SeqNinja automatically translates CDS features rather than the entire sequence. To see a different method of extracting CDS features than was used in Part A and Part B:

1. Open the SeqNinja Text View by clicking the Text tab near the bottom left corner of the SeqNinja window or by choosing View > Text View.

The Text view contains the same information as the Visual View, but in a more concise format. With experience, you may be able to write a script more quickly in the Text View than the Visual View. The Text View is also more efficient than the Visual View when adding large amounts of data, such as lists of sequence sub-ranges, or when copying and pasting, as in our next step.

2. Overwrite the existing text by copying and pasting the text below:

$A = “LAMCG.seq”+“pbr322.seq”+“tethis21.seq” “Translatedgenes.fasta” = translate($A,’/transl_table=11’)

3. To view the revised script in the Visual view, select the Visual tab or use the View > Visual View command.

Note that the extraction step has been eliminated, and the sequence variable is now utilized in the translation step.

This is the end of Tutorial 2.