User:Scientific29/Comparison of Genome Browsers

Name Language Price Web-based, mobile or standalone Notes
Alamut Handles HGVS nomenclature[1] and integrates missense and splicing[2] prediction tools for mutation interpretation.
Annmap Shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data using the 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 Ensembl Genome Browser (Wellcome Trust Sanger Institute and EBI)[7][8]
  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.
  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 151184. 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 3278759. 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 3245178. 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 99161. 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 2995126. 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 3258165. PMID 22102585.
  12. ^ Genome Wowser. "Best Science Apps". Genetic Engineering & Biotechnology News. Feb 01, 2013 (Vol. 33, No. 3).
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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.
  18. ^ 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.
  19. ^ 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.
  20. ^ 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.
  21. ^ 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.
  22. ^ 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.
  23. ^ Zhou, X.; Wang, T. (2012). "Using the Wash U Epigenome Browser to Examine Genome-Wide Sequencing Data". In Andreas D. Baxevanis (ed.). Current Protocols in Bioinformatics. pp. Unit10.Unit10. doi:10.1002/0471250953.bi1010s40. ISBN 0471250953. PMID 23255151.