Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Bioinformatics. 2020 Jun 1;36(11):3573-3575. doi: 10.1093/bioinformatics/btaa192.
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.
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.
Supplementary data are available at Bioinformatics online.
序列 logo 近 30 年前被引入作为表示共识序列的一种易读格式，至今仍被广泛使用。随着新的实验和计算技术的发展，logo 已经得到了扩展：额外的符号表示核苷酸的共价修饰，每个位置有多个字母的 logo 说明了具有多核苷酸特征的模型，x 轴以下延伸的符号可能表示残基的结合能罚分或神经网络的负权重输出。越来越多的基于网络的基因组数据可视化工具利用现代网络技术为用户提供动态、交互式的图形，但对序列 logo 的支持仍然有限。在这里，我们介绍了 LogoJS，这是一个用于呈现可定制、交互式、矢量图形序列 logo 的 JavaScript 包，并将其嵌入到网络应用程序中。LogoJS 支持所有上述 logo 扩展，并附带一个用于创建和共享 logo 的配套网络应用程序。
LogoJS 既可以用纯 JavaScript 实现，也可以用流行的用户界面框架 ReactJS 实现。该网络应用程序托管在 logojs.wenglab.org 上。支持所有主流浏览器和操作系统。该包和应用程序都是开源的；代码可在 GitHub 上获得。
补充数据可在《生物信息学》在线获取。
