Exercise 3: Using the "Transfer Annotations" tool

The transfer annotations tool will appear in the Live annotate & Predict tab if you have selected an alignment file. This tool can also be accessed from the Geneious "Annotate & Predict" menu. This tool works in the same manner as the Annotate From: tool. However, instead of using a database of annotated regions, this tool uses annotated regions found within one or more of sequences within the alignment and compares and matches them to regions within the reference or consensus sequence. The reference sequence can be any sequence in your alignment, and can be defined by right clicking (Alt/Control-click) on a sequence and choosing Set as Reference Sequence.

In this exercise we will again transfer annotations from the emu mitochondrial genome to the kiwi mitochondrial genome.

The basic steps for using this tool.

1. Use an alignment tool to align the sequence you wish to annotate with a homologous sequence that contains the annotations you want to transfer.

2. Use "Set as reference sequence" to designate the sequence you wish to transfer annotations to.

3. Use the Transfer Annotations tool, apply and save.

Exercise 3 - Using Transfer Annotations

In this exercise, as with Exercise 1, we will transfer annotations from the published annotated sequence of the mitochondrial genome of the emu to a "new" unannotated genome of the kiwi.

The sequences are provided with this tutorial and are Named Mitochondrion_Emu and Mitochondrion_Kiwi_3. Select the Two files from the document list, select the Sequence view panel, select the General tab , and make sure the option to Display Annotations is turned on.

The first step before annotation transfer is to align the sequences.

With the two files selected, click on Align/AssemblePairwise align, select the MAFFT aligner and click OK to align the two genomes. This will create an alignment file called Nucleotide Alignment 2. Select this file to view it, then right click on the Mitochondrion_Kiwi_3 sequence and choose Set as Reference sequence.  Save your document.  If you are asked if you wish to apply changes to original sequences.  You should click Yes.

Now go to the Transfer Annotations tool that will have appeared in the Live Annotate and Predict panel .  Drag the slider to reduce the %Similarity stringency until all features are found.  Click Apply to permanently transfer the annotations to the reference sequence, then Save, to save the alignment, and apply the annotations to the parental sequence.

As with the earlier exercises, you should always double check the boundaries of the transferred annotations to make sure they are make sense, and if they are coding sequences, that the translation is correct.

Go to Concluding Summary