Extract Annotated Regions

Using Extract Annotated Regions, parts of a sequence (or several sequences) can be extracted based on annotations. Lengths of flanking regions can be specified if desired. The output is a sequence list that contains sequences carrying the annotation specified.

Some examples of the use of this tool:

To launch Extract Annotated Regions, go to:

        Toolbox | Utility Tools (Image utilities_closed_16_n_p) | Extract Annotated Regions (Image extract_annotations)

This opens the wizard. In the first step (figure 37.1) you can select one or more annotated sequences, annotation tracks, variant tracks, or statistical comparison tracks.

Image extractannotations_genomics_step2
Figure 37.1: Selecting input. Here, statistical comparisontracks have been selected.

If you selected tracks as input, you must enter a reference sequence track in the next wizard step. In that step, you can also specify particular annotations where regions should be extracted, and flanking region lengths to be included, if desired (figure 37.2).

Image extractannotations_genomics_step3
Figure 37.2: Specifying a reference sequence track after track-based data was selected as input.

The sequence of interest can be extracted with flanking sequences:

The sequences that are created can be named after the annotation name, type, etc:

Click Finish to start the tool.