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 25.1) you can select one or more sequences to extract annotated regions from.

Note: With the CLC Main Workbench, annotated sequences are expected as input. Options relating to track-based input are intended for the CLC Genomics Workbench, where this tool is also present.

Image extractannotations_main_step2
Figure 25.1: Select one or more sequences to extract annotated regions from.

At the top of the next dialog step (figure 25.2) you can specify which annotations to use.

Image extractannotations_main_step3
Figure 25.2: Configure the regions for sequence extraction.

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.