Sequence List view
In the Sequence List view (
), you can see sequences at the residue level, or zoomed out to get an overview of the full sequence. Options in the Side Panel to the right allow detailed customization, including aspects like viewing trace data and quality scores, where available (figure 14.7).
Side Panel options
The Side Panel for the Sequence List view shares many options with the Sequence view Side Panel.
- In the Sequence layout palette:
- Align labels. Choose to align the sequence names to the left or right within the sequence label area on the left-hand side of the Sequence List view.
- Under Sequence label, two additional options are available:
- Name (number). Adds sequential numbers after the sequence names.
- (number) Name. Adds sequential numbers before the sequence names.
- Show selection boxes. Check this option to display selection boxes to the left of sequences.
- In the Find palette:
- Name. Search for sequence names. This is useful for searching e.g. sequence lists and mapping results.
Right-click menu options
Right-click on a blank area in a sequence list to access the following options (figure 14.8):
- Extract Sequences (
). Extracts all sequences from the sequence list. If your aim is to extract a subset of the sequences, this can be done from the Table view (
) or using Split Sequence List (
).
- Add Sequences (
). Add sequences from sequence elements or sequence lists to this sequence list.
- Delete All Annotations from All Sequences. Deleting all annotations on all sequences can be done with this option for sequence lists with 1000 or fewer sequences. In other cases, or for more control over the annotations to delete, use the Annotation Table view (
), described further in working with annotations.
Figure 14.8: 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.
Right-click on a sequence or sequence name in a sequence list to access options to (figure 14.9):
- Rename, open, or delete that sequence.
- Sort the sequence list alphabetically by sequence name, length, or marked status (marking of sequences is described below).
These options are only available for sequence lists with 1000 or fewer sequences. Tips for working with larger sequence lists are given in working with large sequence lists.
Figure 14.9: Options to rename, 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.
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 14.10).
Figure 14.10: 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 checked to see these boxes.
To mark sequences:
- In the Side Panel palette Sequence layout on the right hand side, check the Show selection boxes option. This makes checkboxes visible to the right of each sequence name.
- Click in the checkbox beside a sequence name to mark the sequence. Clicking in the checkbox for a marked sequence will remove the mark.
Changing sequence order
The order of sequences in a list can be changed by clicking on the name of the sequence you want to move in the left hand side of the view and dragging and dropping it to the desired position.
When you hover the mouse cursor over the sequence name, the pointer will turn into a vertical arrow, indicating that the sequence can be moved.
To move multiple sequences simultaneously:
- Hold down the Shift key to select adjacent sequences and then drag and drop them to the desired position.
- Hold down the Ctrl key (
on Mac) to select sequences that are not adjacent and then drag and drop them to the desired position.
Selecting parts of sequences in a list
Parts of sequences in a list can be selected as described in selecting parts of the sequence. Selections can be made on multiple different sequences in a list simultaneously (figure 14.11) by:
- Holding down the Shift key while making the selection to make selections with the same start and end positions.
- Holding down the Ctrl key (
on Mac) while making the selection to make selections that have different start and end positions.
Figure 14.11: Selecting parts of multiple different sequences in a list simultaneously. Top: Using the Shift key to make selections with the same start and end positions. Bottom: Using the Ctrl key to make selections with different start and end positions.
Selections on multiple different sequences in a list can e.g. be copied and pasted into external text editing programs. Note, however, that such selections cannot be copied into other sequences or sequence lists in the Workbench. For more information about editing sequence lists by copying and pasting selections, please see editing the sequence.
Subsections