Genome browser

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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[edit]


  1. ^ Laros, J. F. J.; Blavier, A.; Den Dunnen, J. T.; Taschner, P. E. M. (2011). "A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form". BMC Bioinformatics 12: S5. doi:10.1186/1471-2105-12-S4-S5. PMC 3194197. PMID 21992071.  edit
  2. ^ Houdayer, C.; Caux-Moncoutier, V.; Krieger, S.; Barrois, M.; Bonnet, F. O.; Bourdon, V.; Bronner, M.; Buisson, M.; Coulet, F.; Gaildrat, P.; Lefol, C. D.; Léone, M. L.; Mazoyer, S.; Muller, D.; Remenieras, A.; Révillion, F. O.; Rouleau, E.; Sokolowska, J.; Vert, J. P.; Lidereau, R.; Soubrier, F.; Sobol, H.; Sevenet, N.; Bressac-De Paillerets, B.; Hardouin, A. S.; Tosi, M.; Sinilnikova, O. M.; Stoppa-Lyonnet, D. (2012). "Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants". Human Mutation 33 (8): 1228–1238. doi:10.1002/humu.22101. PMID 22505045.  edit
  3. ^ Lewis, S. E.; Searle, S. M.; Harris, N.; Gibson, M.; Lyer, V.; Richter, J.; Wiel, C.; Bayraktaroglir, L.; Birney, E.; Crosby, M. A.; Kaminker, J. S.; Matthews, B. B.; Prochnik, S. E.; Smithy, C. D.; Tupy, J. L.; Rubin, G. M.; Misra, S.; Mungall, C. J.; Clamp, M. E. (2002). "Apollo: A sequence annotation editor". Genome Biology 3 (12): research0082.research0081–82.research0081. doi:10.1186/gb-2002-3-12-research0082. PMC 151184. PMID 12537571.  edit
  4. ^ Engels, R.; Yu, T.; Burge, C.; Mesirov, J. P.; Decaprio, D.; Galagan, J. E. (2006). "Combo: A whole genome comparative browser". Bioinformatics 22 (14): 1782–1783. doi:10.1093/bioinformatics/btl193. PMID 16709588.  edit
  5. ^ Rutherford, K.; Parkhill, J.; Crook, J.; Horsnell, T.; Rice, P.; Rajandream, M. A.; Barrell, B. (2000). "Artemis: Sequence visualization and annotation". Bioinformatics (Oxford, England) 16 (10): 944–945. doi:10.1093/bioinformatics/16.10.944. PMID 11120685.  edit
  6. ^ Carver, T.; Harris, S. R.; Berriman, M.; Parkhill, J.; McQuillan, J. A. (2011). "Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data". Bioinformatics 28 (4): 464–469. doi:10.1093/bioinformatics/btr703. PMC 3278759. PMID 22199388.  edit
  7. ^ Flicek, P.; Amode, M. R.; Barrell, D.; Beal, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; Coates, G.; Fairley, S.; Fitzgerald, S.; Gil, L.; Gordon, L.; Hendrix, M.; Hourlier, T.; Johnson, N.; Kähäri, A. K.; Keefe, D.; Keenan, S.; Kinsella, R.; Komorowska, M.; Koscielny, G.; Kulesha, E.; Larsson, P.; Longden, I.; McLaren, W.; Muffato, M.; Overduin, B.; Pignatelli, M.; Pritchard, B.; Riat, H. S. (2011). "Ensembl 2012". Nucleic Acids Research 40 (Database issue): D84–D90. doi:10.1093/nar/gkr991. PMC 3245178. PMID 22086963.  edit
  8. ^ Hubbard, T.; Barker, D.; Birney, E.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff, J.; Curwen, V.; Down, T.; Durbin, R.; Eyras, E.; Gilbert, J.; Hammond, M.; Huminiecki, L.; Kasprzyk, A.; Lehvaslaiho, H.; Lijnzaad, P.; Melsopp, C.; Mongin, E.; Pettett, R.; Pocock, M.; Potter, S.; Rust, A.; Schmidt, E.; Searle, S.; Slater, G.; Smith, J.; Spooner, W.; Stabenau, A. (2002). "The Ensembl genome database project". Nucleic Acids Research 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMC 99161. PMID 11752248.  edit
  9. ^ Papanicolaou, A.; Heckel, D. G. (2010). "The GMOD Drupal Bioinformatic Server Framework". Bioinformatics 26 (24): 3119–3124. doi:10.1093/bioinformatics/btq599. PMC 2995126. PMID 20971988.  edit
  10. ^ Wang, H.; Su, Y.; MacKey, A. J.; Kraemer, E. T.; Kissinger, J. C. (2006). "SynView: A GBrowse-compatible approach to visualizing comparative genome data". Bioinformatics 22 (18): 2308–2309. doi:10.1093/bioinformatics/btl389. PMID 16844709.  edit
  11. ^ Abeel, T.; Van Parys, T.; Saeys, Y.; Galagan, J.; Van De Peer, Y. (2011). "GenomeView: A next-generation genome browser". Nucleic Acids Research 40 (2): e12. doi:10.1093/nar/gkr995. PMC 3258165. PMID 22102585.  edit
  12. ^ Medina, I.; Salavert, F.; Sanchez, R.; De Maria, A.; Alonso, R.; Escobar, P.; Bleda, M.; Dopazo, J. (2013). "Genome Maps, a new generation genome browser". Nucleic Acids Research 41 (Web Server issue): W41–W46. doi:10.1093/nar/gkt530. PMC 3692043. PMID 23748955.  edit
  13. ^ Genome Wowser. "Best Science Apps". Genetic Engineering & Biotechnology News. Feb 01, 2013 (Vol. 33, No. 3).
  14. ^ Sandve, G. K.; Gundersen, S.; Rydbeck, H.; Glad, I.; Holden, L.; Holden, M.; Liestøl, K.; Clancy, T.; Ferkingstad, E.; Johansen, M.; Nygaard, V.; Tøstesen, E.; Frigessi, A.; Hovig, E. (2010). "The Genomic HyperBrowser: Inferential genomics at the sequence level". Genome Biology 11 (12): R121. doi:10.1186/gb-2010-11-12-r121. PMC 3046481. PMID 21182759.  edit
  15. ^ Lajugie, J.; Bouhassira, E. E. (2011). "GenPlay, a multipurpose genome analyzer and browser". Bioinformatics 27 (14): 1889–1893. doi:10.1093/bioinformatics/btr309. PMID 21596789.  edit
  16. ^ Thorvaldsdottir, H.; Robinson, J. T.; Mesirov, J. P. (2012). "Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration". Briefings in Bioinformatics 14 (2): 178–192. doi:10.1093/bib/bbs017. PMC 3603213. PMID 22517427.  edit
  17. ^ Skinner, M. E.; Uzilov, A. V.; Stein, L. D.; Mungall, C. J.; Holmes, I. H. (2009). "JBrowse: A next-generation genome browser". Genome Research 19 (9): 1630–1638. doi:10.1101/gr.094607.109. PMC 2752129. PMID 19570905.  edit
  18. ^ Jimenez, R. C.; Salazar, G. A.; Gel, B.; Dopazo, J.; Mulder, N.; Corpas, M. (2011). Palau, Francesc, ed. "MyKaryoView: A Light-Weight Client for Visualization of Genomic Data". PLoS ONE 6 (10): e26345. doi:10.1371/journal.pone.0026345. PMC 3202530. PMID 22046276.  edit
  19. ^ Karp, P. D.; Paley, S.; Romero, P. (2002). "The Pathway Tools software". Bioinformatics (Oxford, England). 18 Suppl 1: S225–S232. doi:10.1093/bioinformatics/18.suppl_1.s225. PMID 12169551.  edit
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  21. ^ Goecks, J.; Coraor, N.; Team, T. G.; Nekrutenko, A.; Taylor, J. (2012). "NGS analyses by visualization with Trackster". Nature Biotechnology 30 (11): 1036–1039. doi:10.1038/nbt.2404. PMID 23138293.  edit
  22. ^ Goecks, J.; Eberhard, C.; Too, T.; Nekrutenko, A.; Taylor, J. (2013). "Web-based visual analysis for high-throughput genomics". BMC Genomics 14: 397. doi:10.1186/1471-2164-14-397. PMID 23758618.  edit
  23. ^ Kent, W. J.; Sugnet, C. W.; Furey, T. S.; Roskin, K. M.; Pringle, T. H.; Zahler, A. M.; Haussler, A. D. (2002). "The Human Genome Browser at UCSC". Genome Research 12 (6): 996–1006. doi:10.1101/gr.229102. PMC 186604. PMID 12045153.  edit
  24. ^ Zhou, X.; Maricque, B.; Xie, M.; Li, D.; Sundaram, V.; Martin, E. A.; Koebbe, B. C.; Nielsen, C.; Hirst, M.; Farnham, P.; Kuhn, R. M.; Zhu, J.; Smirnov, I.; Kent, W. J.; Haussler, D.; Madden, P. A. F.; Costello, J. F.; Wang, T. (2011). "The Human Epigenome Browser at Washington University". Nature Methods 8 (12): 989–990. doi:10.1038/nmeth.1772. PMC 3552640. PMID 22127213.  edit
  25. ^ Zhou, X.; Wang, T. (2012). "Using the Wash U Epigenome Browser to Examine Genome-Wide Sequencing Data". In Andreas D. Baxevanis. Current Protocols in Bioinformatics. pp. Unit10.Unit10. doi:10.1002/0471250953.bi1010s40. ISBN 0471250953. PMID 23255151.  edit