Interactive example of overlapping residue annotations. The first sequence has two residue selections indicated by cyan and red
background. The second sequence exhibits two residue selections which are shown as red and green underlining. The text information pops up
when the mouse is moved.
Multiple Sequence Alignments in HTML
Web-interface and API
Create alignment documents with the
Visualization of richly decorated interactive multiple sequence alignments.
Third party software can use Alignment-to-html for alignment computation and visualization.
The HTML alignment files can be viewed in all browsers and on all platforms including Android and iOS and does not require plugins and
is independent of Java.
Client side Java is only required for optional 3D-visualization, 3D-superposition, Jalview and for phylogenetic trees. The client program logic
Meta data like protein name, organism, PDB residue number, PDB insertion code, chain letter, coding triplet, exon number and annotations is
obtained from files in PDB, Swissprot, Embl, Genbank, Nexus and Stockholm format and displayed while the mouse is moved.
Residues can be annotatated directly by commands or by remote BioDAS servers. Send Requests to
Supported platforms: Google-chrome (recommended), Opera, Firefox, Iceweasel, Safari, IE, Epiphany, Konquerer, Android, iOS.
Christoph Gille, Weyand Birgit and Andreas Gille: Sequence alignment visualization in HTML5 without Java (2013) Bioinformatics (30), 121-122
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.
Why without Java?
Java constitutes an additional layer of software and thereby carries an own set of technical problems and risks.
A not in-frequent problem is that Java applets simply fail to run. Since January 2014, the message
Application Blocked By Security Settings or Your security settings have blocked a local application from running is often exhibited with alignment applets like Jalview. In addition
Java bears risks of (I) security threats, (II) browser crashes and (III) memory eating. This was our motivation to develope alignment
visualization platform without plugins or Java.
- Splice variants of hexokinase *
- 3D-superposition of homologous 3D-structures *
- Labels in 3D view *
- BioDAS annotations *
- Using the API: PFAM:PF06446 *
Command line interface
The alignment documents can be generated from the command line
using the Strap scripting language.
Graphical user interface
If you prefer a full featured Java user interface,
then run the program Strap
In Strap open "To HTML for Web pages ..." in the File-menu.