Henry Pratt1, Zhiping Weng1. 1. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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.
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.
Authors: Neva C Durand; James T Robinson; Muhammad S Shamim; Ido Machol; Jill P Mesirov; Eric S Lander; Erez Lieberman Aiden Journal: Cell Syst Date: 2016-07 Impact factor: 10.304
Authors: Aziz Khan; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime A Castro-Mondragon; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada R Kulkarni; Ge Tan; Damir Baranasic; David J Arenillas; Albin Sandelin; Klaas Vandepoele; Boris Lenhard; Benoît Ballester; Wyeth W Wasserman; François Parcy; Anthony Mathelier Journal: Nucleic Acids Res Date: 2018-01-04 Impact factor: 16.971
Authors: Peter Kerpedjiev; Nezar Abdennur; Fritz Lekschas; Chuck McCallum; Kasper Dinkla; Hendrik Strobelt; Jacob M Luber; Scott B Ouellette; Alaleh Azhir; Nikhil Kumar; Jeewon Hwang; Soohyun Lee; Burak H Alver; Hanspeter Pfister; Leonid A Mirny; Peter J Park; Nils Gehlenborg Journal: Genome Biol Date: 2018-08-24 Impact factor: 13.583