You can copy annotations from one sequence to other sequences in the same alignment or assembly document by right-clicking on the annotation and choosing Annotation → Copy to. This will give you the option of either transferring the annotation to the consensus sequence, reference sequence (if there is one), or any of the other sequences in the alignment or assembly. You can also use the associated options: Copy all x to... to copy all annotations of the currently selected annotation type on the selected sequence; and Copy all in selected region to... to copy all annotations in the selected sequence. In each case, the annotation(s) will be copied across regardless of the similarity between the sequences.
Using Transfer Annotations, you can copy annotations to the reference and/or consensus sequence of an alignment or assembly. This function can be accessed from the Annotate and Predict menu, or in the Live Annotate and Predict tab in the sequence viewer. To set a sequence as a reference sequence Ctrl-click on it and choose Set as reference sequence.
Annotations will only be transferred where the annotated sequence and the reference/consensus sequence have at least the speciﬁed minimum similarity. All transferred annotations will be annotated with a Transferred From qualiﬁer indicating the names of the sequences the annotation came from (sorted in order of decreasing similarity), and a Transferred Similarity qualiﬁer which indicates the percentage similarity of the most similar sequence the annotation was transferred from.
Annotations of the same type and covering the same interval that would be transferred from multiple sequences are merged together such that the name of the transferred annotation will consist of the names of all contributing annotations sorted in order of decreasing similarity. Similarly, if contributing annotations have diﬀerent qualiﬁer values, the resulting qualiﬁer value will consist of all contributing qualiﬁer values sorted in order of decreasing similarity.
The percentage similarity is the sum of the similarity values for each position as a fraction of the sum of the maximum similarity values of the bases/residues in each position. For example if one sequence is LLK and the other is LIK using the Blosum62 matrix, L/L scores 4, I/I scores 4, L/I scores 2, K/K scores 5. Therefore the total score is 4+2+5=11 out of a maximum of 4+maximum(4,4)+5=13 for a percentage similarity of 85%. Gaps (if allowed) are scored as the lowest value from the score matrix (e.g. -4 for Blosum62).
Translation properties on CDS annotations are not transferred to the destination sequence. Instead these are renamed to Transferred Translation. The Sequence View calculates and displays an Automatic Translation property on any CDS annotation without a translation. However, this is not a real annotation property that is visible when exported. To add a real Translation property to annotations, use Tools →Workﬂows → Set CDS Translation Property.
Annotate from Database allows you to annotate your sequence with particular genes or motifs from a custom annotation database. The annotation database is a folder (called the Source folder) within your Geneious database which contains sequences with existing annotations (e.g. speciﬁc genes you are interested in searching for on other sequences). This function uses a BLAST-like algorithm to search for annotations in the Source folder that match your sequence. Annotations which match with the given similarity are copied to your sequence. The default annotation folder is the PlasMapper Features folder from the Sample Documents which contains features from the database used by PlasMapper. By default this also annotates Gateway recombination sites. This can be turned oﬀ in the Advanced options.
To use this function:
This will apply any matching annotations that have been found in your annotation database to your sequence(s). If you wish to only apply only some of the annotations to your sequence, select the annotations you want (either directly on the sequence or in the annotations table) before you click Apply. This will apply only the selected annotations onto the sequence rather than all of them.
Annotations with the same type that match the same intervals will be merged in to a single annotation. Merging can be disabled by un-selecting Merge matches with same type and region in the Advanced options.
Note: In Geneious 10.1 onwards protein sequences in your Source folder can be used to annotate nucleotide query sequences. Nucleotide sequences will be translated in all 6 frames for comparison to protein sequences. You can disable this option by unchecking Translation Search in the Advanced options.