title: Sequence alignment visualization in HTML5 without Java.
abstract: BACKGROUND
  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 and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons.
  
  
  CONCLUSIONS
  Alignment-To-HTML, the first interactive alignment visualization that 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 the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software.
  
  
  METHODS
  Under GPL at: http://www.bioinformatics.org/strap/toHTML/.
authors.affiliation: Universitätsmedizin Berlin, Charité, Institut für Biochemie, 10117 Berlin, Germany, Department of Plastic, Hannover Medical School, Hand and Reconstructive Surgery, 30625 Hannover, Germany and Universität Heidelberg, Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, 68169 Mannheim, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Gille
authors.forename: Weyand
authors.initials: W
authors.lastname: Birgit
authors.forename: Andreas
authors.initials: A
authors.lastname: Gille
mesh_terms: D000595:Amino Acid Sequence; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000032:analysis*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins