APPLICATIONS NOTE
Vol. 30 no. 1 2014, pages 121-122 doi:10.1093/bioinformatics/btt614
Sequence analysis Advance Access publication November 21,2013
Sequence alignment visualization in HTML5 without Java
Christoph Gille1[1], Weyand Birgit2 and Andreas Gille3,y
'Universitatsmedizin Berlin, Charite, Institut fUr Biochemie, 10117 Berlin, Germany, 2Department of Plastic, Hannover Medical School, Hand and Reconstructive Surgery, 30625 Hannover, Germany and 3Universitat Heidelberg, Institut fUr Experimentelle und Klinische Pharmakologie und Toxikologie, 68169 Mannheim, Germany
Associate Editor: Martin Bishop
ABSTRACT
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 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.
Conclusion: 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.
Availability and implementation: Under GPL at: http://www.bioinfor matics.org/strap/toHTML/.
Contact: christoph.gille@charite.de
Received on September 10, 2013; revised on October 11, 2013; accepted on October 19, 2013
1 INTRODUCTION
The amount of experimental sequence-related data, such as posttranslational modifications, ligand binding and genetic variants is rapidly growing. Efficient web-based visualization facilitates understanding of the biological meaning of comprehensive data sets. Advanced visualization of multiple sequence alignments (MSA) includes sequence-related information such as residue annotation, color-coding of physical properties of residues,secondary structure and conservation/variation. A number of programs have been developed for non-interactive rendering of MSAs: Alscript (Barton, 1993), Boxshade, Espript (Gouet et al., 2003) and TexShade (Beitz, 2000). These programs generate an alignment figure according to a script file. The script can be prepared manually in a text editor or dynamically by another program. Therefore, these programs are suited to display computational results of web services. The generated alignment figures use vector graphics formats for quality reasons, but most browsers do not support vector image formats (e.g. SVG) and external document viewers are required. A further disadvantage is that these figures are static and lack interactivity. Interactive capabilities, hyperlinks, baloon messages and the option to shield information become increasingly important in the omics era.
Java brought interactive functionality to web pages and allows alignment manipulation in real time (Caffrey et al., 2007; Clamp et al., 2004; Lord et al., 2002). Owing to its cross-platform compatibility, integrated graphics and high execution speed, Java is widely used.
But there are also five potential problems: (i) failure to start Java applications, (ii) security violations, (iii) browser crashes, (iv) incompatibility on some platforms such as Android OS and (v) slowing of the computer. Today the web standard HTML5 is being increasingly used for interactive web applications such as genome browsers (Hoy, 2011; Medina et al., 2013; Miller et al., 2013). The main advantage is that HTML5 code is executed directly in the browsers without additional client side software. A potential challenge with HTML5 code is that its execution is slow, and we were wondering whether it would be sufficient for full-featured MSA visualization.
2 IMPLEMENTATION
Our alignment visualization system consists of two parts: (i) A server side non-interactive program generates a graphical representation of the MSA in HTML according to an input text file. (ii) A comprehensive JS-library encoding the interactive graphical user interface for the HTML page.
Canvas elements allow for dynamic scriptable rendering of 2D shapes and are used for secondary structure cartoons. If they are not supported, the secondary structure is symbolized by text characters. For maximum cross-browser compatibility, residues are draw
剩余内容已隐藏，支付完成后下载完整资料
资料编号：[139620]，资料为PDF文档或Word文档，PDF文档可免费转换为Word
以上是毕业论文外文翻译，课题毕业论文、任务书、文献综述、开题报告、程序设计、图纸设计等资料可联系客服协助查找。
