User:Scientific29/Comparison of Genome Browsers

Source: Wikipedia, the free encyclopedia.
Name Language Price Web-based, mobile or standalone Notes
Alamut Handles HGVS nomenclature
missense and splicing[2] prediction tools for mutation
interpretation.
Annmap Shows
Leafletjs
Maps API
Apollo Genome Annotation Curation Tool Java Standalone [3]
Argo Genome Browser Java Free [4]
Artemis Genome Browser Free Desktop
Wellcome Trust Sanger Institute) for visualizing and manually annotating whole genomes.[5] It can also be used to visualize next generation 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 Desktop Especially suited for comparing prokaryotic genomes.
Celera Genome Browser Free Developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.
Chipmonk Java To visualise and analyse ChIP-on-chip array data, developed at the Babraham Institute in Cambridge.
Dalliance Javascript
DiProGB: The Dinucleotide Properties Genome Browser
DNAnexus Flash Also next-gen sequence analysis and visualization.
Ensembl The
Wellcome Trust Sanger Institute and EBI)[7][8]
  • 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]
  • Genome Savant - visual analytics
  • GenomeView is a next-generation stand-alone genome browser and editor specifically designed to visualize and manipulate a multitude of genomics data. [11]
  • HuRef - stand-alone browser for navigating individual human genome
  • 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.[12]
  • The Genomic HyperBrowser focuses on statistical analysis of elements along the genome;[13] 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.[14]
  • 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 [15]
  • 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.[16]
  • MGV - Microbial Genome Viewer
  • myKaryoView - A Direct-to-consumer oriented genomic browser [17]
  • 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[18]
  • 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
  • TGAC Browser visualisation solutions for big data in the genomic era. An open-source Genome Browser developed at The Genome Analysis Centre, UK works with Ensembl Data set and many more.
  • Trackster Galaxy's visualization and visual analysis environment [19] [20]
  • UCSC Genome Bioinformatics Genome Browser and Tools (UCSC)[21]
  • 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[22][23]
  1. PMID 21992071.{{cite journal}}: CS1 maint: unflagged free DOI (link
    )
  2. PMID 22505045
    .
  3. PMID 12537571.{{cite journal}}: CS1 maint: unflagged free DOI (link
    )
  4. PMID 16709588
    .
  5. PMID 11120685
    .
  6. PMID 22199388
    .
  7. PMID 22086963
    .
  8. PMID 11752248
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  9. PMID 20971988
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  10. PMID 16844709
    .
  11. PMID 22102585
    .
  12. ^ Genome Wowser. "Best Science Apps". Genetic Engineering & Biotechnology News. Feb 01, 2013 (Vol. 33, No. 3).
  13. PMID 21182759.{{cite journal}}: CS1 maint: unflagged free DOI (link
    )
  14. PMID 21596789
    .
  15. PMID 22517427
    .
  16. PMID 19570905
    .
  17. PMID 22046276.{{cite journal}}: CS1 maint: unflagged free DOI (link
    )
  18. PMID 12169551
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  19. PMID 23138293
    .
  20. PMID 23758618.{{cite journal}}: CS1 maint: unflagged free DOI (link
    )
  21. PMID 12045153
    .
  22. PMID 22127213
    .
  23. PMID 23255151
    .
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