Transfer Annotations by Homology

Introduction

Annotations provide descriptive information about the structure and/or function of features within DNA, RNA or protein sequences. Annotations may sometimes be grouped into "tracks" and sometimes span multiple intervals, for example, when a CDS comprises multiple exons.

Geneious has several tools and third-party plugins for adding new annotations to sequences, most can be found under the Annotate and Predict menu. This tutorial focuses on the Transfer Annotations function, which is useful for transferring features to a reference or consensus sequence in an alignment or assembly, where homology is shared across some or all regions of the alignment.

To learn about other methods of transferring annotations check out these other pages:

► Transfer Annotations from Database

► Transfer Annotations by Alignment

► Annotate Sequences Video Series

Annotations are the equivalent of "Features" found in GenBank files. See our Knowledge Base post for more information on standard annotations/features used in Geneious and GenBank.

Install Plugin

This tutorial requires the MAFFT alignment plugin. To install, go to Menu Tools → Plugin and choose MAFFT Multiple Alignment from the list of Available Plugins.

Using the Transfer Annotations Tool

The transfer annotations tool will appear in the Live annotate and Predict tab if you have selected an alignment file. This tool can also be accessed from the Geneious "Annotate and 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 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.

Transfer Annotations

In this exercise, 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/Assemble → Pairwise 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 all annotations transfers, 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.

Summary

Geneious Prime offers three Annotation-transfer methods any one of the three methods could be used to do the same job with the same data-set. The tool you decide to use depends in part on whether you are working with closely or distantly related sequences and whether you have homologous annotated sequences suitable for transfer by alignment.

Please consult the Geneious Manual Transfer Annotations Section for further information on transfer of annotations.