8.1.4 Extracting Annotations

To extract an annotation to a separate document, select it either on the sequence or in the annotations table and click Extract. If you want to actively link the extracted annotation to the source document (so that changes on the source document are propagated to the extracted document), check Actively link source and extracted documents.

If the annotation you are extracting contains multiple intervals, the intervals can be concatenated into a single sequence. If this option is not selected, then each interval in the annotation will be extracted to a separate sequence and grouped into a list.

Bulk extraction

Bulk extraction of annotations can be done in two ways:

1. Select all the annotations you want to extract, either on the sequence or in the Annotations table and click Extract. As with multi-interval annotations, you are given the option to concatenate all the annotations into a single sequence.
2. Go to Extract Annotations under the Tools menu. Using this interface, all annotations on the selected sequences which match certain criteria (e.g. a particular annotation type or gene name) can be extracted in bulk, without needing to select the annotations on the sequence first. To define what annotations to extract, select the value of the annotation type or property (qualifier) that you want to extract by in the chooser (see Figure 8.5 ). To set more than one criteria, click the + button to add an additional row of options, and choose to either Match all... or Match any... of the criteria.

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   Figure 8.5: The Extract Annotations Interface

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   What to Extract allows you to set which part of the sequence to extract (e.g. just the annotated region, or the entire sequence) based on the criteria you have set. To extract regions of sequence upstream or downstream of the annotated sequence, enter the length of the additional sequence you want to extract under Extraction Context. Intersecting Annotations allows you to set what to do with other annotations that don’t match the criteria, but which overlap with the matched region.

   If there are multiple annotations on one sequence which match the criteria, these can be concatenated into one sequence by checking Concatenate regions within each sequence.