5.5 Translating sequences

The protein translation can be viewed alongside the nucleotide sequence by checking the Translation option in the PIC Display tab. Select the genetic code and reading frame(s) you require. You can also choose to translate relative to selection or annotations such as CDS (Figure 5.5 ). In an alignment, the sequence frame can be calculated relative to the individual sequences, the alignment, the consensus or a specific reference sequence. On a contig or alignment, the translation can be displayed on the consensus and reference sequence only, or it can be displayed on all sequences.

There is a checkbox to show three letter rather than single letter amino acids. Translations which have two possibilities will always show as single letter amino acids. e.g. V/M. For stand-alone protein sequences, there is no option whether to show three letter codes or not. Instead, three letter codes are automatically displayed when the zoom level is 200% or higher and when not in editing mode.

If you wish to view only the translation and turn off the nucleotide sequence, uncheck Nucleotides. However, this is only for display purposes: if you wish to work with the translation in downstream analysis you must extract it to a separate document using the Translate button above the sequence viewer. The Translate button will create new protein document from the translated DNA, using your choice of reading frame and genetic code. This option can also be accessed from the Sequence menu.

To copy the translation of a selected region of a nucleotide sequence, right click on the selected sequence and choose Copy Translation from the menu. The copied translation can then be pasted into the New Sequence box or into a document outside of Geneious.


Figure 5.5: Translating a CDS

   5.5.1 Genetic Codes
   5.5.2 Back Translating