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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W3-6. doi: 10.1093/nar/gku400. Epub 2014 May 9.

Alignment-Annotator web server: rendering and annotating sequence alignments.

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Department of Biochemistry, Charité, University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
Institute of Vegetative Physiology, Charité, University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany.
Department of Plastic, Hand and Reconstructive Surgery, Hannover Medical School, Carl-Neubergstraße 1, 30625 Hannover, Germany.
Mannheim Medical Faculty, Institute of Experimental and Clinical Pharmacology and Toxicology, Heidelberg University, Maybachstraße 14, 68169 Mannheim, Germany.


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. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. 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. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. 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. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization.


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