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Related Experiment Video

Updated: May 5, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Sequence alignment visualization in HTML5 without Java.

Christoph Gille¹, Weyand Birgit, Andreas Gille

¹Universitätsmedizin 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.

Bioinformatics (Oxford, England)

|November 26, 2013

Summary

This summary is machine-generated.

Alignment-To-HTML is a novel web-based tool for visualizing biological sequence alignments without Java. This HTML5-based system offers interactive features for complex biological data display in all browsers.

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Area of Science:

Bioinformatics
Computational Biology
Web Technologies

Background:

Java applets have been widely used for web-based biological data visualization.
Java's runtime environment presents technical challenges and security risks.
HTML5 offers features that can potentially replace Java for certain visualization tasks.

Purpose of the Study:

To develop an interactive visualization tool for annotated multiple sequence alignments using HTML5.
To demonstrate that HTML5 is sufficient for displaying complex biological data in web browsers.
To provide a Java-free alternative for biological data visualization.

Main Methods:

Developed Alignment-To-HTML, a server-side script interpreter.
Implemented sequence retrieval, alignment computation, and rendering functionalities.
Ensured compatibility across all browsers and platforms, including touch screen tablets.

Main Results:

Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments.
The tool supports interactive features like drag-and-drop reordering, highlighting, and interlinked 3D visualization.
Novel features include support for overlapping residue annotations, export to MS-Word, and sequence icons.

Conclusions:

HTML5 is capable of displaying complex biological data, reducing the need for Java.
Browser execution speed remains a limitation for complex interactive applications.
The study anticipates increased use of HTML and JavaScript for interactive biological software.