Sequence Lists

Sequence list elements contain one or more nucleotide sequences or one or more peptide sequences. They are used as input to many tools, and are generated as output by many tools. Sequence lists can contain single end sequences or paired end sequences, but not a mixture of both. Handling paired data is described at the end of this section.

The icons at the bottom of an open view of a sequence list view provide access to different representations, i.e. different views, of the data. In figure 13.17, the graphical view and tabular view of the same sequence list are shown in a split view.

Image sequencelist-twoviews
Figure 13.17: Two views of the same sequence list open in a horizontally split view, the graphical view at the top, and a tabular view at the bottom. Each view can be customized using settings in the right hand side panel.

Creating sequence lists

Sequence lists are created in various ways, including:

Working with the graphical view

The graphical view of sequence lists offers many of the same viewing options as for individual sequence elements. These are described in Viewing and editing sequences. In addition, context menus with options relevant to managing sequence lists appear when you right-click on areas of the graphical view of a sequence list. For example:

To rename multiple sequences in a list following the same renaming pattern, consider using the Rename Sequences in Lists tool, described in sequence Rename Sequences in Lists.

Working with the table view

In the table view of a sequence list (figure 13.18), various attributes that pertain to each sequence are listed. This includes information like:

Some of these attributes can be changed (for example, Name), while others are calculated from the sequence itself (e.g. Length, First 50 residues) and so cannot be directly edited.

The number of rows reported at the top of the table view is the number of sequences in the list. With one or more rows selected, the Create New Sequence List button is enabled, so a new list containing those sequence can easily be made.

Standard functionality for working with tables applies, as described in Working with tables.

Image sequencelists-table-view
Figure 13.18: In table view, each sequence in a list is presented in a row. The number of rows is reported at the top left side.

Adding sequences to an existing sequence list can be done by dragging and dropping sequences or sequence lists from the Navigation Area into the table view.

Sequences can be removed by highlighting the relevant rows in the table and clicking on the Delete (Image delete_document_2_16_n_p) icon in the top toolbar.

Sequences can be extracted from a sequence list by:

Working with paired sequences in lists

When paired sequence data is imported, the resulting sequence list will be marked as containing paired data. This information can be seen in the Element info view, as described in Element information.

Sequence lists can only contain single ended data or paired end data. A single sequence list cannot contain a mixture of these.

To create a paired sequence list from existing sequence lists, for example by merging lists, the input lists must be marked as paired and must have the same distance settings. If the input lists do not meet these criteria, a message is shown warning that the resulting sequence list will be unpaired (figure 13.19). Paired status and distance settings can be edited in the Element info view (figure 13.20).

Image sequencelistwarning
Figure 13.19: A warning appears when trying to create a new sequence list from a mixture of paired and unpaired sequence lists.

Image sequencelistedit
Figure 13.20: The paired status as well as the minimum and maximum distance settings for a sequence list can be edited in the Element info view.