Graphical view of sequence lists

In the graphical view of sequence lists, you can see sequences at the residue level, or zoomed right out to get an overview of the full sequence. Options in the Side Panel on the right allow detailed customization, including aspects like viewing trace data and quality scores, where available (figure 15.1).

Much of the functionality available when working with sequence lists is also available when working with individual sequence elements. Shared functionality is described in Viewing and editing sequences. This section describes options relevant only to sequence lists.

Menus available when you right-click give access to much functionality for manipulating sequence lists.

Right-click on a blank area to access the following options (figure 15.2):

Right-click on a sequence or sequence name to access options (figure 15.3) to:

Tips for working with larger sequence lists are given later in this section.

Marking sequences:

Sequences in a list can be marked. Once marked, those sequences can be deleted, or the sequence list can be sorted based on whether sequences are marked or not. It is easy to adjust markings on many sequences using the options in the right-click menu on selection boxes (figure 15.4).

To mark sequences:

  1. Check the Show selection boxes option in the "Sequence List Settings" section of the side panel settings on the right hand side.

    This makes checkboxes visible to the right of each sequence name.

  2. Click in the checkbox beside a sequence name to mark the sequence.

    Clicking in the box for a marked sequence will remove the mark.

Image seqlist-rtclick-onblank
Figure 15.2: Options to extract the sequences in the list, add sequences to the list, and to delete all annotations on all sequences are available when you right-click on a blank area of the graphical view of a sequence list.

Image seqlist-rtclick-ontext
Figure 15.3: Options to rename, select, open, or delete a sequence are available when you right-click on the name or residues for a given sequence. Also in this menu are options for sorting the list and deleting marked sequences.

Image seqlist-invert-all-marks
Figure 15.4: Which sequences are marked can be quickly adjusted using the options in the right-click menu for any selection checkbox. The Show Selection boxes option in the side panel must be enabled to see these boxes.

Tips when working with large sequence lists