Genome browser

In bioinformatics, 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

• Alamut A gene browser that handles HGVS nomenclature^[1] and integrates missense and splicing^[2] prediction tools for mutation interpretation.
• Annmap A genome browser that shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data using the Leafletjs 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.^[3]
• Argo Genome Browser A free and open-source standalone Java-based genome browser for visualizing and manually annotating whole genomes.^[4]
• Artemis Genome Browser A free and open-source standalone genome browser (Wellcome Trust Sanger Institute) for visualizing and manually annotating whole genomes.^[5] It can also be used to visualize next generation sequencing data.^[6]
• 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.
• Chipmonk A Java-based tool to visualise and analyse ChIP-on-chip array data, developed at the Babraham Institute in Cambridge.
• Dalliance Javascript-based genome browser
• 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 (Wellcome Trust Sanger Institute and EBI)^[7][8]
• ERGO The ERGO Bioinformatics Suite developed by Igenbio, Inc
• Gaggle Genome Browser A java-based genome browser developed at Institute for Systems Biology (ISB) for high-throughput data integration.
• GeneWall - Mobile genome browser
• GBrowse The GMOD GBrowse Project^[9][10]
• Genestack web-based genomics operating system
• GenomeView is a next-generation stand-alone genome browser and editor specifically designed to visualize and manipulate a multitude of genomics data.^[11]
• Genome Maps implements HTML5, scalable vector graphics, displaying genes, transcripts, exons, regulatory features, SNPs etc. Allows the local upload of large genomic data files.^[12]
• Genome Wowser An iPad-enabled view of the human genome. The app, developed by the Center for Biomedical Informatics (CBMi) at The Children's Hospital of Philadelphia, provides a functional presentation of the popular UCSC Genome Browser.^[13]
• HuRef - stand-alone browser for navigating individual human genome
• The Genomic HyperBrowser focuses on statistical analysis of elements along the genome;^[14] built on the Galaxy platform.
• Genostar GenoBrowser: a standalone application to display and explore genomic data from any kind of file (EMBL, GenBank, Fasta, GFF...)
• Genoverse interactive genome browser: web-based, scrollable genome browser, designed to be easily integrated into any website with a few strings of javascript. Loads data dynamically via AJAX and visualizes via HTML5 canvas element
• GenPlay A genome viewer and analyzer developed in Java at Albert Einstein College of Medicine.^[15]
• Golden Helix GenomeBrowse A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.
• Integrated Genome Browser (IGB) Open-source and free Java-based desktop genome viewer for visualizing next-gen sequence and microarray data.
• Integrative Genomics Viewer IGV A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.^[16] A lite version for the iPad is available in the Apple App Store.
• 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.^[17]
• Maverix Biomics Genome Browser (commercial)
• MGV - Microbial Genome Viewer
• myKaryoView - A Direct-to-consumer oriented genomic browser ^[18]
• 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^[19]
• Persephone Next-generation genome visualization and exploration software.^[20]
• Plant GDB - Plant genome browser
• Savant Genome Browser for visual analytics of high-throughput sequencing data
• SEED viewer for visualizing and interrogating the SEED database of complete microbial genomes
• STAR: An Integrated Solution to Management and Visualization of Sequencing Data
• Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.^[21]
• TGAC Browser visualisation solutions for big data in the genomic era. An open-source Genome Browser developed at Earlham Institute, UK works with Ensembl Data set and many more.
• Trackster Galaxy's visualization and visual analysis environment ^[22][23]
• UCSC Genome Browser and Tools (UCSC Genome Bioinformatics) at UC Santa Cruz).^[24] Browser for more than 240 genomes: vertebrates and model invertebrates.
• UGENE visualizes sequences and annotations on a local computer
• 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.
• WashU EpiGenome Browser web-based visual exploration of genomics and epigenomics data sets^[25][26]
• CGView

References

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