Genome browser

A genome browser is a graphical interface for display of information from a biological database for genomic data. Genome browsers enable researchers to visualize and browse entire genomes (most have many complete genomes) with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. Annotated data is usually from multiple diverse sources. They differ from ordinary biological databases in that they display data in a graphical format, with genome coordinates on one axis and the location of annotations indicated by a space-filling graphic to show the occurrence of genes, etc.

List of genome browsers

• Annmap A genome browser that shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data on a Google Maps API
• Apollo Genome Annotation Curation Tool A cross-platform, Java-based standalone genome viewer with enterprise-level functionality and customizations. The standard for many model organism databases.
• Argo Genome Browser A free and open source standalone Java-based genome browser for visualizing and manually annotating whole genomes.
• Avadis NGS combines a genome browser and set of data analysis tools for ChIP-Seq, RNA-Seq, and genomic variation experiments, developed by Strand Life Sciences
• BugView Free cross-platform desktop browser for visualizing genomes, especially suited for comparing prokaryotic genomes.
• Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.
• DiProGB: The Dinucleotide Properties Genome Browser
• DNAnexus Flash-based interactive genome browser, as well as next-gen sequence analysis and visualization.
• Ensembl The Ensembl Genome Browser (Sanger Institute and EBI)
• Gaggle Genome Browser A java-based genome browser developed at Institute for Systems Biology (ISB) for high-throughput data integration.
• GBrowse The GMOD GBrowse Project
• The Genomic HyperBrowser focuses on statistical analysis of elements along the genome.
• Genostar GenoBrowser: a standalone application to display and explore genomic data from any kind of file (EMBL, GenBank, Fasta, GFF...)
• GenPlay A genome viewer and analyzer developed in Java at Albert Einstein College of Medicine.
• Integrated Genome Browser (IGB) Open source and free Java-based desktop genome viewer for visualizing next-gen sequence and microarray data.
• Integrated Microbial Genomes (IMG) system by the DOE-Joint Genome Institute
• JBrowse a JavaScript genome browser by the open source Generic Model Organism Database project.
• MGV - Microbial Genome Viewer
• MochiView Genome Browser
• NextBio Genome Browser - an interactive application that lets visualization of physical relationship between private or public biosets and different types of genomic elements, including genes, miRNA targets, CNVs, CpG islands, SNPs, GWAS associations, and LD blocks]
• Pathway Tools Genome Browser
• SEED viewer for visualizing and interrogating the SEED database of complete microbial genomes
• UCSC Genome Bioinformatics Genome Browser and Tools (UCSC)
• Viral Genome Organizer (VGO) A genome browser providing visualization and analysis tools for annotated whole genomes from the eleven virus families in the VBRC (Viral Bioinformatics Resource Center) databases
• VISTA genome browser a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.