How to construct and manipulate a structural alignment?

You have: a structural alignment.
You want: to play with it!!

In this tutorial, you will learn how to:

Once a structural alignment loaded (for more details, see the tutorial "how to load data into Assemble2?"), it is displayed in the lateral panel named "Structural Alignment". It displays all the sequences aligned against the reference sequence (and labeled 'S1'), which is folded and displayed in the main panel.

This panel allows you to contruct/improve a structural alignment interactively for a set of orthologous RNA sequences. Using colored structural masks, it will help you to identify base-pair covariations, leading to the characterization of a consensus secondary structure.

If the reference sequence ('S1') is linked to a tertiary structure, this panel allows you to derive it into a new RNA 3D model for one of the sequences aligned (for more details, see the tutorial "How to derive a new 3D structure from a solved 3D?").

From top to bottom, a structural alignment is made with:

  • a ruler for the alignment,
  • a bracket notation describing the consensus secondary structure for all the sequences in the alignment,
  • a bracket notation describing the secondary structure for the reference sequence (labeled as 'S1'). This bracket notation is a 1D notation of the secondary structure displayed in the main panel,
  • the reference sequence for the alignment (labeled as 'S1'). It corresponds to the sequence you have selected when you have loaded your data. You can choose a different reference sequence with the icon gears icon in the Alignment toolbar
  • all the other sequences.

The consensus bracket notation is editable and describes:

  • unpaired residues with the character '.'
  • paired residues with the characters '(' and ')'
The reference bracket notation is not editable and describes:
  • unpaired residues with the character '.'
  • paired residues in helices with the characters '(', ')', '[', ']', '{' and '}' (as in the lateral panel "Secondary Structure")

Manipulate a structural alignment

You can interact with your structural alignment using:

Browse the alignment

The lateral panel "Structural Alignment" splits the alignment into two views that can be manipulated independently. You can:

Keep the left mouse button pressed on a view...
... and drag the mouse to move along the alignment.

Or you can:

Left-click on a residue to select the view...
... and use the keys 'E' or 'R' to move faster along the alignment.

Browse genomic sequences

If you have opened a GFF3 or a Genbank file, and loaded one of the genomic annotation, two arrows are displayed at each end of the alignment.

By left-clicking on one of them,...
...you can walk along the genomic sequence and have a look at the genomic neighbourhood of your RNA annotation.

Select residues

Left click on a residue to select it.
If you [Shift] + left click on a second one, all the residues in between will be selected.
Residues selected in the reference sequence (S1) will be automatically selected in the secondary structure (and in the 3D if you have one).

Modify a structural alignment

Move residues

To move residues, select them as described above...
... and use the keys 'O' or 'P' to translate them on the left or on the right.

Add/remove gaps

Consecutive left clicks on an alignment position in the ruler...
...will add columns of gaps after this position.
A left click on an alignment position corresponding to a column of gaps...
...will remove it.

Change the bracket notations

Each consecutive left-click on a position of the bracket notation...
...will allow you to iterate over...
...the characters '(', ')' and '.'.
You can note that, after each mouse click, a new structural mask is computed from the consensus bracket notation (observable only if you have chosen this mask with eye icon in the alignment toolbar).

The bracket notation for the reference structure cannot be modified from the structural alignment. You have to edit the secondary structure directly from the main panel (for details, see the tutorial "How to edit an RNA secondary structure?").

Fabrice Jossinet, PhD | University of Strasbourg, ARN | UPR 9002 of CNRS | f[dot]jossinet[at]ibmc-cnrs[dot]unistra[dot]fr