SynTView — an interactive multi-view genome browser for next-generation comparative microorganism genomics

BMC Bioinformatics

Pierre Lechat¹  Erika Souche²  Ivan Moszer¹ 

[1] Institut Pasteur, Plate-forme Bioanalyse Génomique, 28 rue du Docteur Roux, Paris, Cedex 15 75724, France

[2] Current address: Laboratory for Molecular Diagnosis, KU Leuven, O&N I Herestraat 49, B-3000, Leuven, Belgium

关键词: Interactive graphical user interface;    Flash;    Single Nucleotide Polymorphism (SNP);    Next-Generation Sequencing (NGS);    Synteny;    Microbial genomics;    Genome browser;   

Others  :  1087759
DOI  :  10.1186/1471-2105-14-277

 received in 2013-03-25, accepted in 2013-09-16,  发布年份 2013

【 摘 要 】

Background

Dynamic visualisation interfaces are required to explore the multiple microbial genome data now available, especially those obtained by high-throughput sequencing — a.k.a. “Next-Generation Sequencing” (NGS) — technologies; they would also be useful for “standard” annotated genomes whose chromosome organizations may be compared. Although various software systems are available, few offer an optimal combination of feature-rich capabilities, non-static user interfaces and multi-genome data handling.

Results

We developed SynTView, a comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects (annotations). The software is characterised by the presentation of syntenic organisations of microbial genomes and the visualisation of polymorphism data (typically Single Nucleotide Polymorphisms — SNPs) along these genomes; these features are accessible to the user in an integrated way. A variety of specialised views are available and are all dynamically inter-connected (including linear and circular multi-genome representations, dot plots, phylogenetic profiles, SNP density maps, and more). SynTView is not linked to any particular database, allowing the user to plug his own data into the system seamlessly, and use external web services for added functionalities. SynTView has now been used in several genome sequencing projects to help biologists make sense out of huge data sets.

Conclusions

The most important assets of SynTView are: (i) the interactivity due to the Flash technology; (ii) the capabilities for dynamic interaction between many specialised views; and (iii) the flexibility allowing various user data sets to be integrated. It can thus be used to investigate massive amounts of information efficiently at the chromosome level. This innovative approach to data exploration could not be achieved with most existing genome browsers, which are more static and/or do not offer multiple views of multiple genomes. Documentation, tutorials and demonstration sites are available at the URL: http://genopole.pasteur.fr/SynTView webcite.

【 授权许可】

   
2013 Lechat et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

【 参考文献 】

• [1]Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ: High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 2012, 10:599-606.
• [2]Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB: The real cost of sequencing: higher than you think! Genome Biol 2011, 12:125. BioMed Central Full Text
• [3]Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T: Visualizing genomes: techniques and challenges. Nat Methods 2010, 7:S5-S15.
• [4]Baker S, Hanage WP, Holt KE: Navigating the future of bacterial molecular epidemiology. Curr Opin Microbiol 2010, 13:640-645.
• [5]Köser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ: Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012, 8:e1002824.
• [6]Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y: GenomeView: a next-generation genome browser. Nucleic Acids Res 2012, 40:e12.
• [7]Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA: BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011, 12:402. BioMed Central Full Text
• [8]Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA: Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012, 28:464-469.
• [9]Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J: DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009, 25:119-120.
• [10]Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell BG, Parkhill J, Rajandream MA: Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008, 24:2672-2676.
• [11]Darling AE, Mau B, Perna NT: progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5:e11147.
• [12]Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M: Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res 2012, 40:W615-W621.
• [13]Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32:W273-W279.
• [14]Grant JR, Arantes AS, Stothard P: Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics 2012, 13:202. BioMed Central Full Text
• [15]Herbig A, Jager G, Battke F, Nieselt K: GenomeRing: alignment visualization based on SuperGenome coordinates. Bioinformatics 2012, 28:i7-15.
• [16]Kerkhoven R, Van Enckevort FH, Boekhorst J, Molenaar D, Siezen RJ: Visualization for genomics: the Microbial Genome Viewer. Bioinformatics 2004, 20:1812-1814.
• [17]Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645.
• [18]Louis A, Muffato M, Roest Crollius H: Genomicus: five genome browsers for comparative genomics in eukaryota. Nucleic Acids Res 2012, 41:D700-D705.
• [19]Meyer M, Munzner T, Pfister H: MizBee: a multiscale synteny browser. IEEE Trans Vis Comput Graph 2009, 15:897-904.
• [20]Pan X, Stein L, Brendel V: SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics 2005, 21:3461-3468.
• [21]Pedersen BS, Tang H, Freeling M: Gobe: an interactive, web-based tool for comparative genomic visualization. Bioinformatics 2011, 27:1015-1016.
• [22]Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G: Interactive microbial genome visualization with GView. Bioinformatics 2010, 26:3125-3126.
• [23]Revanna KV, Chiu CC, Bierschank E, Dong Q: GSV: a web-based genome synteny viewer for customized data. BMC Bioinforma 2011, 12:316. BioMed Central Full Text
• [24]Riley DR, Angiuoli SV, Crabtree J, Dunning Hotopp JC, Tettelin H: Using Sybil for interactive comparative genomics of microbes on the web. Bioinformatics 2012, 28:160-166.
• [25]Sinha AU, Meller J: Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinforma 2007, 8:82. BioMed Central Full Text
• [26]Sullivan MJ, Petty NK, Beatson SA: Easyfig: a genome comparison visualizer. Bioinformatics 2011, 27:1009-1010.
• [27]Thorvaldsdottir H, Robinson JT, Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2012. doi:10.1093/bib/bbs017
• [28]Uchiyama I, Higuchi T, Kobayashi I: CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. BMC Bioinforma 2006, 7:472. BioMed Central Full Text
• [29]Wang H, Su Y, Mackey AJ, Kraemer ET, Kissinger JC: SynView: a GBrowse-compatible approach to visualizing comparative genome data. Bioinformatics 2006, 22:2308-2309.
• [30]Apache Flex. http://flex.apache.org/ webcite
• [31]Flare: Data Visualization for the Web. http://flare.prefuse.org/ webcite
• [32]GenoList: Integrated Environment for the Analysis of Microbial Genomes. http://genolist.pasteur.fr/GenoList webcite
• [33]Lechat P, Hummel L, Rousseau S, Moszer I: GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Res 2008, 36:D469-D474.
• [34]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
• [35]Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, Von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD: Rapid pneumococcal evolution in response to clinical interventions. Science 2011, 331:430-434.
• [36]Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD: Cytoscape Web: an interactive web-based network browser. Bioinformatics 2010, 26:2347-2348.
• [37]Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P: iPath2.0: interactive pathway explorer. Nucleic Acids Res 2011, 39:W412-W415.
• [38]MEDEA: Comparative Genomic Visualization with Adobe Flash. http://www.broadinstitute.org/annotation/medea webcite
• [39]Ondov BD, Bergman NH, Phillippy AM: Interactive metagenomic visualization in a Web browser. BMC Bioinforma 2011, 12:385. BioMed Central Full Text
• [40]Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW: On the origins of a Vibrio species. Microb Ecol 2010, 59:1-13.
• [41]Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, De Lencastre H, Parkhill J, Peacock SJ, Bentley SD: Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.