ALGORITHMS AND SOFTWARE ImplementationĪlignment-Annotator has been implemented in PHP, which uses the Java program Alignment-To-HTML to generate the HTML code ( 11). In following these trends, we have designed Alignment-Annotator as a web service to create interactive multiple decorated sequence alignments in HTML5. Interestingly, in contrast to the client side, there is the trend of Java usage on the server side. For this reason, HTML5 has been developed as the new standard for web browsers to natively support multimedia and graphical content. In addition there are risks of (i) security threats, (ii) browser crashes and (iii) excessive memory consumption. A not in-frequent problem is that Java applets simply fail to run. However, Java constitutes an additional layer of software and thereby carries an own set of technical problems and risks. Java applets have overcome these shortcomings and have brought real-time interactivity and 3D visualization for alignments ( 8–10). Interactive capabilities including hyper-links, balloon messages and the option to shield information are becoming increasingly important in the -omics era. A further and more important shortcoming is that these documents lack interactivity. However, vector images are not commonly supported by web browsers without additional plugins. PostScript, PDF and SVG which can be displayed and printed on all computer platforms in high quality. These programs generate high quality figures as vector graphics e.g. ALSCRIPT ( 5), BoxShade, ESPript ( 6) and TexShade ( 7). This is surprising because software already exists for this task, e.g. UniProt ( 1), Pfam ( 2), SCOPe ( 3) and T-Coffee ( 4). Many of these applications offer their own implementation for server side alignment rendering, e.g. There already exist multiple web services that utilize or provide sequence alignments. Sequence alignment visualization is a widely used method to indicate differences and similarities in bio-polymers and to elucidate structurally and functionally important sequence positions. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. The final alignment document can be downloaded as a zip-archive containing the HTML files. Some edits take immediate effect while others require server interaction and may take a few seconds to execute. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. ![]() Interactivity is implemented in HTML5, a language native to web browsers. All computations are performed at server side. Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software.
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