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LogoJS: a Javascript package for creating sequence logos and embedding them in web applications.

ABSTRACT:

Summary

Sequence logos were introduced nearly 30 years ago as a human-readable format for representing consensus sequences, and they remain widely used. As new experimental and computational techniques have developed, logos have been extended: extra symbols represent covalent modifications to nucleotides, logos with multiple letters at each position illustrate models with multi-nucleotide features and symbols extending below the x-axis may represent a binding energy penalty for a residue or a negative weight output from a neural network. Web-based visualization tools for genomic data are increasingly taking advantage of modern web technology to offer dynamic, interactive figures to users, but support for sequence logos remains limited. Here, we present LogoJS, a Javascript package for rendering customizable, interactive, vector-graphic sequence logos and embedding them in web applications. LogoJS supports all the aforementioned logo extensions and is bundled with a companion web application for creating and sharing logos.

Availability and implementation

LogoJS is implemented both in plain Javascript and ReactJS, a popular user-interface framework. The web application is hosted at logojs.wenglab.org. All major browsers and operating systems are supported. The package and application are open-source; code is available at GitHub.

Contact

zhiping.weng@umassmed.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Pratt H

PROVIDER: S-EPMC7267833 | biostudies-literature |

REPOSITORIES: biostudies-literature

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