Annotated multiple sequence alignments in web pages

Example alignment including annotations and 3D-structure

Left snapshot: By clicking amino acids in the alignment, the respective position in 3D is indicated. Right snapshot: vice versa. In both cases, the rendering style of the picked amino acid or atom can be changed or a text label attached.


Look at the alignment in the figure. The secondary structure is shown above the sequence rows. Observe balloon messages over protein names, secondary structure cartoons and residue underlinings. For the first sequence the accession ID is known and the asterisk acts as a database link. Residue selections are shown either as colored background or lines below the sequence. Optionally they have a balloon message.

Would you like to include alignments like this into your project page? With Strap it is simple.


Preparing alignments for web browsers

  1. Prepare the alignment HTML document. Three options:
  2. Insert the alignment into your web site with iframe HTML tags.
              <iframe src="http://.../my_aligment.html" width="400" height="400" name="alignment" scrolling="auto"  >


3D-visualization requires Java and may not work in all browsers/platforms. Currently, iPads and Android tablets are not able to run the Open-Astex 3D viewer. The option to visualize the 3D-structure is automatically included for all sequences that are loaded from PDB. For amino acid sequences not loaded from a PDB file, 3D visualization can be enabled by associating a homologous 3D-structures. Either click the tool-button "3D" or use the 3D-menu of the context menu (right click). When the HTML alignment is exported from Strap, all 3D-views (Pymol, Open-Astex or Jmol) with more than one 3D-model give rise to a 3D start button in the alignment HTML export. In the browser version always Open-Astex will be used, irrespectively of the 3D-visualization software currently opened in Strap. The menu of the 3D view in Strap is displayed with black background to be distinguishable from the main menu. Using the menu "Superimpose", all displayed peptide chains can be aligned three-dimensionally. Using "Color" in the "Style"-menu, the color of the entire peptide chain can be specified. Conversely, labels, color and 3D styles of atoms will not be directly inferred into the browser version. For rendering certain amino acids or atoms, residue selections need to be defined in Strap. Those residue selections can carry 3D-style commands. These 3D-styles are applied.

Exons and coding triplets

If amino acid sequences are translated from nucleotide sequences, the coding triplet, nucleotide positions and exon number is reported for the amino acid under the pointer. This is the case when EMBL or Genbank formated files are loaded. If the coding sequence is not interrupted by introns, it is likely to be cDNA or bacterial DNA rather than genomic eucaryotic DNA. In this case the exon information is not displayed. The following alignment contains all splice variants of Hexokinase. Move the mouse pointer and observe the coding triplet and nucleotide position displayed together with the amino acid number.