Genome browser

From Wikipedia, the free encyclopedia
Jump to: navigation, search

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]

References[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 3194197free to read. PMID 21992071. 
  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. 
  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 151184free to read. PMID 12537571. 
  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. 
  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. 
  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 3278759free to read. PMID 22199388. 
  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 3245178free to read. PMID 22086963. 
  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 99161free to read. PMID 11752248. 
  9. ^ Papanicolaou, A.; Heckel, D. G. (2010). "The GMOD Drupal Bioinformatic Server Framework". Bioinformatics. 26 (24): 3119–3124. doi:10.1093/bioinformatics/btq599. PMC 2995126free to read. PMID 20971988. 
  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. 
  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 3258165free to read. PMID 22102585. 
  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 3692043free to read. PMID 23748955. 
  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 3046481free to read. PMID 21182759. 
  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. 
  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 3603213free to read. PMID 22517427. 
  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 2752129free to read. PMID 19570905. 
  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 3202530free to read. PMID 22046276. 
  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. 
  20. ^ http://www.bio-itworld.com/2014/4/25/persephone-real-time-genome-browser.html
  21. ^ Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D (2013). "Using Tablet for visual exploration of second-generation sequencing data". Briefings in Bioinformatics. 14 (2): 193–202. doi:10.1093/bib/bbs012. PMID 22445902. 
  22. ^ 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. 
  23. ^ 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. 
  24. ^ 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 186604free to read. PMID 12045153. 
  25. ^ 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 3552640free to read. PMID 22127213. 
  26. ^ 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.