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Table 5 Genome browsers

From: Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Tool and references

Description

URL

Web-based or standalone

ABrowse [231]

A customizable genome browser framework

http://www.abrowse.org/

Web-based

AnnoJ [232]

A web 2.0 application designed for visualizing deep sequencing data and other genome annotation data

http://www.annoj.org/

Web-based

Argo

Java tool for visualizing and manually annotating whole genomes

http://www.broadinstitute.org/annotation/argo/

Standalone

Artemis [104]

Browser and annotation tool that allows visualization of sequence features, data and the results of analyses within the context of the sequence, and also its six-frame translation

https://www.sanger.ac.uk/resources/software/artemis/

Standalone

CGView [233]

Static and interactive graphical maps of circular genomes using a circular layout

https://www.gview.ca/wiki/GView/

Standalone

Combo [234]

Dynamic browser to visualize alignments of whole genomes and their associated annotations

http://www.broad.mit.edu/annotation/argo/

Standalone

Ensembl [105, 106]

Annotation, analysis and display of vertebrates and other eukaryotic species

http://www.ensembl.org/

Web-based

Family Genome Browser [235]

Visualizing genomes with pedigree information

http://mlg.hit.edu.cn/FGB/

Web-based

Gaggle [236]

Genome browser within an analysis framework; good microarray support

http://gaggle.systemsbiology.net/

Standalone

GBrowse [237, 238]

A combination of database and interactive web pages for manipulating and displaying annotations on genomes

http://gmod.org/wiki/Gbrowse

Web-based

GenoMap [239]

A circular genome data viewer

http://nsato4.c.u-tokyo.ac.jp/old/GenoMap/GenoMap.html

Standalone

Genome Projector [240]

Circular genome maps, traditional genome maps, plasmid maps, biochemical pathways maps and DNA walks. Google API

http://www.g-language.org/GenomeProjector/

Web-based

GenomeView [241]

Designed to visualize and manipulate a multitude of genomics data

http://genomeview.org/content/integration

Standalone

GenPlay [242]

A multipurpose genome analyzer and browser

http://www.genplay.net

Standalone

IGB [243]

Optimized to achieve maximum flexibility and high quality genome visualization

http://genoviz.sourceforge.net/

Standalone

IGV [222]

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets

http://www.broadinstitute.org/igv/

Standalone

JBrowse [244]

A fast, embeddable genome browser built completely with JavaScript and HTML5

http://jbrowse.org/

Web-based

JGI

Supports live annotation; primary portal for DOE Joint Genomics Institute genome projects

http://genome.jgi-psf.org/

Web-based

NCBI Genome Workbench

An integrated application for viewing and analyzing sequence data

http://www.ncbi.nlm.nih.gov/tools/gbench/

Standalone

NCBI Map Viewer [245]

Vertically oriented viewer; integrated with NCBI resources and tools

http://www.ncbi.nlm.nih.gov/mapview/

Web-based

Phytozome [246]

A comparative platform for green plant genomics

http://www.phytozome.net

Web-based

Savant [247]

It was primarily developed for visualizing sequencing data, although it can be used to visualize almost any genome-based sequence, point, interval or continuous dataset

http://compbio.cs.toronto.edu/savant

Standalone

Scribl [248]

An HTML5 Canvas-based graphics library for visualizing genomic data over the web

http://chmille4.github.com/Scribl/

Web-based

The HuRef Browser [249]

A web resource for individual human genomics

http://huref.jcvi.org

Web-based

The personal genome browser [250]

Visualizing functions of genetic variants

http://www.pgbrowser.org/

Web-based

UCSC Cancer Genomics Browser [251, 252]

Integration of clinical data

http://genome-cancer.ucsc.edu/

Web-based

UCSC Genome Browser [103]

Rapid linear visualization, examination and querying of the data at many levels

http://genome.ucsc.edu/cgi-bin/hgGateway

Web-based

UTGB [253]

Open-source software for developing personalized genome browsers that work in web browsers

http://utgenome.org/

Web-based

X:map [254]

Mappings between genomic features and Affymetrix microarrays

http://xmap.picr.man.ac.uk/

Web-based