Analysis and Visualisation of Protein Secondary Structure Annotations

Jalview has a number of specialised capabilities for working with protein secondary structure annotation linked to aligned sequences.

When one or more sequences with secondary structure annotations are present on the alignment, Jalview automatically displays Secondary Structure Consensus annotation tracks, to assess the proportion of Helix, Sheet or Coil annotations for aligned positions in each column. Conensus tracks can also be shown for particular sources of structural data (e.g. from jnet, the PDB, AlphaFold or SWISS-MODEL), and are calculated over all the secondary structure tracks for a sequence, allowing visualisation of diversity across multi-chain structures that contain more than one copy of the sequence.

Like with sequence consensus and conservation tracks, it is also possible shade a group of sequences or the whole alignment to highlight regions of secondary structure conservation and divergence with Secondary Structure Consensus colouring.

Visualising the secondary structure 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 two or more secondary structure annotations are available for sequences in the alignment. Moving the mouse over the label of a consensus row displays a tooltip that reports both the number of sequences, and the number of secondary structure annotations that were included in the consensus calculation.

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. These settings can be adjusted by right-clicking the Secondary Structure Consensus' label to open it's annotation track popup menu.

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.

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

Protein secondary structure tends to be more conserved than sequence, and Jalview allows calculation of trees based on secondary structure annotation to visualise which secondary structure tracks (and thus, which sequences) are more structurally similar. The leaves in secondary structure trees are linked to both a sequence and one of its secondary structure annotation tracks, allowing secondary structures and aligned sequences to be partitioned into groups. Secondary structure diversity can be visualised for each group by application of Secondary Structure Consensus Colouring.

Visualisation of differences between sources of secondary structure data

Visualisations of secondary structure trees can be labelled or shaded according to provider (i.e. the source of secondary structure annotation), by enabling one of the options in Show Secondary Structure Providers. Groups defined by partitioning trees are also labeled by provider.

The screenshot below shows an alignment grouped by secondary structure similarity and coloured by 'Sequence ID colour'. Secondary Structure Consensus shading has also been enabled, highlighting regions where secondary structure is not conserved.

The tree also shows coloured lines corresponding to provider, visualising how the secondary structures from each source differs from others.