8.3 Compare Annotations

Geneious Prime can compare annotations across up to 3 annotation tracks or documents, highlighting annotations which are common or unique depending on which criteria you choose.

To use this function, select the sequence or sequences containing annotations you wish to compare, and go to Annotate and Predict → Compare Annotations. In the Annotation Types panel, select the annotations you wish to compare. The default setting is for pairwise comparison; if you wish to do three-way comparison select Set C. Choose the annotation type and location for each set, and the type of comparison.

Comparison options are:

• Names must match: The names of the annotations must be the same. When allowing partial matches for polymorphism annotations, just the name of the matching region of the annotation must match.
• All properties must match: All properties in addition to the name must be the same to be considered a match
• Allow intervals to partially match: When one annotation partially overlaps another, you can choose to return either Partial Annotations or Full Annotations. Partial Annotations will return annotations spanning or excluding only the matching region. Full Annotations will return annotations spanning the entire length of the applicable source annotation. Uncheck this option if you only want to return annotations which match across the full length of both sets.

Results

A new annotation track will be created showing the results of the comparison. The results panel in the compare annotations set up allows you to choose which comparison to return:

• A-B-C returns annotations found only in set A
• B-A-C returns annotations found only in set B
• C-A-B returns annotations found only in set C
• A&B&C returns annotations common to all sets. For a pairwise comparison, when the annotation is common to both sets the result will have the name and type of annotation from set A but share properties from both sets if selected. For a three-way comparison properties from set A will be used.

More than one of these options can be selected at once, either by checking the box next to the option, or clicking the appropriate section of the venn diagram to the right. Each result comparison is displayed on a separate track on the original sequence, and a preview of these tracks is given in the Example panel.

Example 1 - finding polymorphisms within a gene or feature (e.g. CDS, restriction site)

To return a track containing polymorphism annotations that are within another gene or feature, such as a coding sequence, select the Polymorphism annotation type for Set A, and choose which track it is on (or select anywhere if there are no tracks, or you want to include polymorphisms on any track). Then choose the other annotation type (e.g. CDS) for Set B. Uncheck Names must match as in general polymorphism annotation names do not match those of other annotation types, and check Allow intervals to partially match and produce partial annotations. Under Results, choose to return A & B (annotations common to both sets). This will return a new track containing annotations of the type in Set A (polymorphisms) that are contained within Set B (CDS) annotations. See Figure 8.9 .

Example 2 - finding polymorphisms in a child which are not present in either parent

To return polymorphisms which are unique to the offspring, set Annotation Type as Polymorphism for Sets A, B and C, and set A and B as the parent tracks, and C as the child track, as in Figure 8.10 . Check Names must match and Allow intervals to partially match and produce partial annotations. Choose C-A-B in the results display. This will return a new track containing annotations found in Set C (child), but not in Sets A and B (parents).