Pimp your RNA secondary structure

The new daily build (Oct 1st, 2013) introduces and improves features allowing you to map “information” on your RNA secondary structure.

Assign quantitative and qualitative values

You can now map and visualize qualitative and quantitative experimental data (SHAPE, chemical probing, solvent accessibility,…) on your RNA secondary structure. The file format to be used is a text file, where each line is made up of two fields: the absolute position (from 1 to the size of the molecule) and its qualitative or quantitative value. Both fields have to be separated with one or several spaces or a semi-colon ‘;’. An example with quantitative values :

16;0.321682458
17;0.600862135
18;0.071343178
19;0.20473273
20;0.096093561

…an other example with qualitative values:

16 +++
17 +
18 --
19 ++
20 +++

… and a last one:

16 good
17 bad
18 good
19 excellent
20 bad

The lines don’t need to be sorted and some positions can be missing. Assemble2 displays non-assigned positions with a dedicated color (see below).

Once your 2D structure opened and displayed in Assemble2, open the lateral panel named “Secondary Structure”, right-click on the 2D node and choose “Assign quantitative data”:

quantitative

or “Assign qualitative data”.

qualitative

You can switch between the different displays by using the show/hide options available from the popup menu.

The colors for the min and max values (quantitative data) or for each category (qualitative data) can be changed with the menus “Edit->Colors->Quantitative Data” or “Edit->Colors->Qualitative Data”.  A color can also be defined for the non-assigned positions (“No Value” color).

When quantitative data are displayed, you can double-click on the color gradient to define its min and max values. This allows you to map the color gradient to a new range of values. If you compare with the previous screenshot, i have now set the max value to 0.2. All the residues with a value above this max are now colored in red.

quantitative_2

Display the consensus structural mask

When you open a secondary structure (predicted from an RNA sequence, pre-computed and stored in a CT or BPSEQ file, or computed from a 3D structure), Assemble2 displays it in in the main and central panel.  In the lateral panel named “Structural alignment”, this secondary structure has been derived into two bracket notations:

  • the consensus bracket notation: it is editable and extensible. It allows you to define the structure common to several related RNA sequences,
  • the reference bracket notation:  the bracket notation for the 2D displayed in the main panel and corresponding to the sequence S1 in the alignment.

Each bracket notation can produce a structural mask. A structural mask is used to check if your alignment conserve or not the base-pairing defined by the bracket notation selected.  From the lateral panel “Structural alignment”, you can select the structural mask to be used. If you choose the structural mask for the “Consensus Bracket notation”, you will see that Assemble2 has assigned a different color for each helix computed from the consensus bracket notation.

consensus_mask

If you right-click on the 2D node in the lateral panel “Secondary Structure”, you can choose “Display consensus mask” to visualize these colors directly on your 2D structure:

consensus_mask_2

If you dislike the colors chosen, you can define new ones by clicking on the brush icon in the lateral panel “Structural alignment”.

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