Table 4.
Genome browsers and biological data visualization libraries
| Name | Description | URL |
|---|---|---|
| 1000 Genomes browser | Genome browser to access data from 1000 Genomes project. | http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/ |
| AnnoJ | Web 2.0 application designed for visualizing sequencing and annotation data. | http://www.annoj.org/ |
| Artemis | Genome Browser and Annotation Tool. | http://www.sanger.ac.uk/resources/software/artemis/ |
| Bio::Graphics | Perl modules for biological data visualization. | http://search.cpan.org/dist/Bio-Graphics/ |
| Bio::Graphics (Ruby) | Ruby library for drawing overviews of genomic regions. | http://bio-graphics.rubyforge.org/ |
| Bluejay | Java-based integrated computational environment for the exploration of genomic data. | http://bluejay.ucalgary.ca/ |
| CGView | Circular Genome Viewer. | http://wishart.biology.ualberta.ca/cgview/ |
| Circos | Circos is a software package for visualizing genomic data and annotations in circular layout. | http://circos.ca/ |
| Dalliance | Interactive genome viewer, which runs directly in a modern web browser. | http://www.biodalliance.org/ |
| DAS | DAS is an integrated visualization toolkit to share and collate genomic annotation information. | www.biodas.org |
| DASTY | Web client for visualizing protein sequence feature information using DAS. | http://www.ebi.ac.uk/dasty/ |
| DNAPlotter | DNAPlotter can be used to generate images of circular and linear DNA maps to display regions and annotations of interest. | http://www.sanger.ac.uk/resources/software/dnaplotter/ |
| Ensembl Genome Browser | Ensembl Genome Browser enables the visualization of genomic and transcriptomic sequence and related information for several vertebrate and non-vertebrate species. | http://useast.ensembl.org/index.html |
| GASV | Geometric Analysis of Structural Variants. | http://compbio.cs.brown.edu/software.html |
| Gbrowse | Generic Genome Browser (GBrowse) is a genome viewer developed as part of Generic Model Organism Database (GMOD) project. | http://gmod.org/wiki/GBrowse |
| GENBOREE | Customizable genome browser. | http://genboree.org/java-bin/login.jsp |
| GeneViTo | JAVA-based workbench for genome-wide analysis through visual interaction. | http://athina.biol.uoa.gr/bioinformatics/GENEVITO/ |
| GenomeGraphs | R-based interface to plot genomic information from Ensembl. | http://www.bioconductor.org/packages/release/bioc/html/GenomeGraphs.html |
| GenomePixelizer | Tool to generate custom images of genomes out of the given set of genes. | http://www.atgc.org/GenomePixelizer/ |
| GenomeTools | Versatile genome analysis software. | http://genometools.org/ |
| GenomeView | Next-generation stand-alone genome browser and editor. | http://genomeview.org |
| Gremlin | Interactive visualization model for analyzing genomic rearrangements. | http://compbio.cs.brown.edu/software.html |
| IGB | Integrated genome browser. | http://bioviz.org/igb/index.html |
| IGV | Integrative Genomics Viewer. | http://www.broadinstitute.org/igv/ |
| Jbrowse | Genome browser with a fully dynamic AJAX interface. | http://gmod.org/wiki/JBrowse |
| jsDAS | JavaScript client library for the DAS. | http://www.ebi.ac.uk/dasty/ebi/html/jsdas.html |
| MagicViewer | Integrated solution for NGS data visualization and genetic variation detection and annotation. | http://bioinformatics.zj.cn/magicviewer/index.php |
| NCBI Graphical Sequence Viewer | Graphical display for the Nucleotide and Protein sequences. | http://www.ncbi.nlm.nih.gov/projects/sviewer/ |
| Rover | Genome browser framework to build custom genomic tools. | http://chmille4.github.com/Rover/site/home.html |
| Rviewer | Interactive online tool for comparing and prioritizing genomic regions. | http://rviewer.lbl.gov/rviewer/ |
| Savant | Genome Browser for high-throughput sequencing data. | http://genomesavant.com/ |
| Scribl | HTML5 Canvas-based graphics library for visualization of genomic data and annotations. | http://chmille4.github.com/Scribl/ |
| UCSC Genome Browser | Interactive genome browser that provide access to sequence data from different species, integrated with a large collection of layered annotations from experiments and prediction algorithms. | http://genome.ucsc.edu/cgi-bin/hgGateway |
| VISTA Browser | Visualization of pairwise and multiple alignments of whole genome assemblies. | http://pipeline.lbl.gov/cgi-bin/gateway2?selector=vista |
| Whole Genome rVISTA | Visualization of TFBS that are conserved between species and overrepresented in upstream regions of groups of genes. | http://genome.lbl.gov/vista/index.shtml |