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]
- 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 The Genome Analysis Centre, 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 100 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
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ Genome Wowser. "Best Science Apps". Genetic Engineering & Biotechnology News. Feb 01, 2013 (Vol. 33, No. 3).
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ http://www.bio-itworld.com/2014/4/25/persephone-real-time-genome-browser.html
- ↑ Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, Shaw PD and 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
This article is issued from Wikipedia - version of the Monday, January 04, 2016. The text is available under the Creative Commons Attribution/Share Alike but additional terms may apply for the media files.