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.
In Geneious Prime, annotations are displayed graphically in the Sequence Viewer panel where they can be edited and their display can be controlled via the Annotations & Tracks tab . Annotations are depicted graphically as boxes or as arrows if the feature has a defined orientation.
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.
Geneious has numerous tools and third-party plugins for adding new annotations to sequences, most of which can be found under the Annotate and Predict menu. This tutorial focuses only on methods for transferring existing annotations between sequences.
Transferring annotations allows you to quickly annotate a sequence using features annotated on related sequences.
There are three ways to transfer annotations between sequences within Geneious, which can be summarised as being either:
by alignment - Using "Copy To..." - Useful for transferring individual annotations or for shorter alignments where homology is shared across the entire length of the alignment
by homology - Using "Annotate From" Using a custom
feature database - useful for annotating unaligned sequences with a
diverse selection of features
by homology - Using "Transfer Annotations" - 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
This tutorial provides exercises demonstrating how to use each of the above methods. Click on the links below to go to each exercise directly, or start with Exercise 1 to work through all three exercises.
This tutorial requires the MAFFT alignment plugin. If you do not already have it installed, the go to Geneious Menu Tools → Plugins... and install the MAFFT Multiple Alignment tool from the list of Available Plugins.
Click on the links below to go to the exercises.
Exercise 1: Transferring annotations using "Copy to..."
Exercise 2: Live annotation using "Annotate From"
Exercise 3: Live annotation using "Transfer Annotations"
Summary: Summary