Table 5.
Genome browsers
| 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 |