Sequence alignment visualization in HTML5 without Java

Motivation: Java has been extensively used for the visualization of biological data in the web. However, the Java runtime-environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary. Results: ALIGNMENT-TO-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server-side script interpreter can perform all tasks like (I) sequence retrieval (II) alignment computation (III) rendering (IV) identification of a homologous structural models and (V) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets color schemes, highlighting of conserved and variable alignment positions, row reordering by drag&drop, interlinked 3D-visualization and sequence groups. Novel features are (I) support for multiple overlapping residue annotations, such as chemical modifications, SNPs and mutations. (II) mechanisms to quickly hide residue annotations, (III) export to MS-Word, and (IV) sequence icons. Conclusion: ALIGNMENT-TO-HTML, the first interactive alignment visualization which runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still main obstacles. Nevertheles, we envision an increased use of HTML and Java-Script for interactive biological software