Translating Nucleotide Sequence

When a nucleotide sequence is opened in the Sequence View, both the sequence and its complementary sequence are displayed by default in the Details View.

Showing/Hiding the Amino Acid Sequences

It is possible to translate them and also show the corresponding amino acid sequences:

The translation settings are available on the left toolbar of the Details View:

The Show/Hide Amino Acid Translations menu allows you to set up the mode for amino acid sequence visualization:

The following options are available:

  • Do not translate — hide the amino acid sequences.
  • Translate selection — translate only a selected region of the sequence and the complementary sequence.

  • Set up frames manually — select the reading frames to display. There are three frames for the sequence ("+1", “+2”, “+3”) and three for the complementary sequence ("-1", “-2”, “-3”). Note that the complementary frame items are hidden in the menu if the complementary sequence is hidden.

  • Show all frames — show all amino acid sequences.

Setting the Genetic Code

The default value for the genetic code for nucleotide sequence translation is read by UGENE from the sequence file when it is available. You can also set up the genetic code for the sequence using the Select Genetic Code menu:

All analysis routines (such as HMMER, ORF finding, etc.) will use this code by default.

Codon Table

To refresh your knowledge about the amino acid codes, select the Show Codon Table button on the Sequence View global toolbar. The codon table appears at the upper part of the window:

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