Protein Secondary Structure Consensus Annotation

Since version 2.11.4.0, Jalview can automatically calculate consensus secondary structure for an alignment of protein sequences where one or more sequences have secondary structure annotation, in the same way as is done with the sequence consensus.

To view secondary structure consensus rows, you should first enable the Secondary Structure checkbox in Jalview Preferences. Once this option is checked, a consensus row will be shown if secondary structure annotations are available for two or more sequences in the alignment.

Sources of secondary structure data

Sequences can have several different secondary structure annotations, including those provided by observed or computationally determined 3D structures, or predicted by JPred. Sequence associated secondary structure annotations can also be imported as Jalview Annotation files. Secondary structure annotations for a particular source can be shown or hidden via Annotations→Show Secondary Structure menu option in the alignment window.

Consensus Secondary Structure

The secondary structure consensus can be shown as a histogram, reflecting the proportion of the most frequent conformation observed in a column, optionally overlaid with a logo to reflect the distribution of observed structure. The Alignment window's Annotations→Autocalculated Annotation includes options for controlling the appearance of the secondary structure consensus row, and whether rows should be shown for groups defined on the alignment.