Neugebauer, Tomasz 
ORCID: https://orcid.org/0000-0002-9743-5910, Bordeleau, Eric, Burrus, Vincent and Brzezinski, Ryszard
(2015)
DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes.
PLOS ONE, 10
(12).
e0143615.
ISSN 1932-6203
Preview |
Text (application/pdf)
7MBjournal.pone.0143615.pdf |
Official URL: http://dx.doi.org/10.1371/journal.pone.0143615
Abstract
Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.
| Divisions: | Concordia University > Library |
|---|---|
| Item Type: | Article |
| Refereed: | Yes |
| Authors: | Neugebauer, Tomasz and Bordeleau, Eric and Burrus, Vincent and Brzezinski, Ryszard |
| Journal or Publication: | PLOS ONE |
| Date: | 2015 |
| Funders: |
|
| Digital Object Identifier (DOI): | 10.1371/journal.pone.0143615 |
| Keywords: | Data visualization, Chromosomes, Nucleotide sequencing, Bacterial genomics, Genome analysis, Ribosomal RNA, DNA sequence analysis |
| ID Code: | 980761 |
| Deposited By: | Tomasz Neugebauer |
| Deposited On: | 21 Dec 2015 18:03 |
| Last Modified: | 18 Jan 2018 17:51 |
| Related URLs: |
References:
1. Isenberg P, Elmqvist N, Scholtz J, Cernea D, Ma KL, Hagen H. Collaborative visualization: definition, challenges, and research agenda. Inf Vis. 2011;10:310–326. doi: 10.1177/1473871611412817.2. Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Visualizing genomes: techniques and challenges. Nat Methods. 2010;7:S5–S15. doi: 10.1038/nmeth.1422. pmid:20195257
3. Makino S, Naoki A, Suzuki M. Visual presentation of complete genomic DNA sequences, and its application to identification of gene-coding regions. Proc Japan Acad. 1999;75(10): Ser. B. doi: 10.2183/pjab.75.311.
4. Yoshida T, Obata N, Oosawa K. Color-coding reveals tandem repeats in the Escherichia coli genome. J Mol Biol. 2000;298: 343–349. doi: 10.1006/jmbi.2000.3667. pmid:10772854
5. Seaman JD, Sanford JC. Skittle: a 2-dimensional genome visualization tool. BMC Bioinformatics. 2009;10:452. doi: 10.1186/1471-2105-10-452. pmid:20042093
6. DNA rainbow [Internet]. Available: http://www.dna-rainbow.org
7. Dnaskittle [Internet]. Available: http://dnaskittle.com/
8. Microsoft .NET Framework 4 (Web Installer) [Internet]. Available: http://www.microsoft.com/en-ca/download/details.aspx?id=17851
9. OpenSeadragon [Internet]. Available: http://openseadragon.github.io/
10. BioJS library of JavaScript components to represent biological data [Internet]. Available: https://github.com/biojs/biojs
11. D3.js–Data Driven Documents [Internet]. Available: http://d3js.org/
12. Civetweb embedded c/c++ web server [Internet]. Available: https://github.com/sunsetbrew/civetweb
13. PHP [Internet]. The PHP Group. Available: http://www.php.net/
14. Képès F, Jester BC, Lepage T, Rafiei N, Rosu B, Junier I. The layout of a bacterial genome. FEBS Lett. 2012;586:2043–2048. doi: 10.1016/j.febslet.2012.03.051. pmid:22483986
15. Picardeau M, Lobry JR, Hinnebusch B. Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome. Mol Microbiol. 1999;32: 437–445. doi: 10.1046/j.1365-2958.1999.01368.x. pmid:10231498
16. Lobry JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol. 1996;13: 660–665. Available: http://mbe.oxfordjournals.org/content/13/5/660.full.pdf+html pmid:8676740
17. Wright F, Bibb MJ. Codon usage in the G+C-rich Streptomyces genome. Gene. 1992; 113: 55–65. doi: 10.1016/0378-1119(92)90669-G. pmid:1563633
18. Hopwood DA. Soil to genomics: the Streptomyces chromosome. Ann Rev Genet. 2006; 40: 1–23. doi: 10.1146/annurev.genet.40.110405.090639. pmid:16761950
19. Pernodet JL, Bocard F, Alegre MT, Gagnat J, Guérineau M. Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens. Gene. 1989;79: 33–46. doi: 10.1016/0378-1119(89)90090-5. pmid:2777089
20. Zarko-Postawka M, Hunderuk M, Mordarski M, Zakrzewska-Czerwinska J. Organization and nucleotide sequence analysis of the ribosomal gene set (rrnB) from Streptomyces lividans. Gene. 1997;185:231–237. doi: 10.1016/S0378-1119(96)00649-X. pmid:9055820
21. Bentley SD, Chater KF, Cerdeño-Tàrraga AM, Challis GL, Thomson NR, James KD, et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002;417:141–147. doi: 10.1038/417141a. pmid:12000953
22. French S. Consequences of replication fork movement through transcription units in vivo. Science. 1992;258:1362–1365. doi: 0.1126/science.1455232 pmid:1455232 doi: 10.1126/science.1455232
23. Rocha EPC, Danchin A, Viari A. Universal replication biases in bacteria. Mol Microbiol. 1999;32:11–16. doi: 10.1046/j.1365-2958.1999.01334.x. pmid:10216855
24. Weaver D, Karoonuthaisiri N, Tsai HH, Huang CH, Ho ML, Gai S, et al. Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome. Mol Microbiol. 2004;51:1535–1550. doi: 10.1111/j.1365-2958.2003.03920.x. pmid:15009883
25. Wlodarczyk M, Giersz D. [Linear plasmids of bacteria]. Post Mikrob. 2006;45:5–18. Polish.
26. Jankowitsch F, Schwarz J, Rückert C, Gust B, Szczepanowski R, Blom J, et al. Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. J Bacteriol. 2012;194:6818–6827. doi: 10.1128/JB.01592-12. pmid:23043000
27. Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005;3:722–732. doi: 10.1038/nrmicro1235. pmid:16138100
28. Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet. 2006, 38:779–786. doi: 10.1038/ng1830. pmid:16804543
29. Brouwer MS, Warburton PJ, Roberts AP, Mullany P, Allan E. Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile. PLoS One. 2011;6:e23014. doi: 10.1371/journal.pone.0023014. pmid:21876735
30. Burrus V, Pavlovic G, Decaris B, Guedon G. The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration. Plasmid. 2002;48:77–97. doi: 10.1016/S0147-619X(02)00102-6. pmid:12383726
31. Farrow KA, Lyras D, Rood JI. Genomic analysis of the erythromycin resistance element Tn5398 from Clostridium difficile. Microbiology. 2001;147:2717–2728. Available: http://mic.sgmjournals.org/content/147/10/2717.full.pdf+html pmid:11577151
32. Eichler EE, Clark RA, She X. An assessment of the sequence gaps: unfinished business in a finished human genome. Nature Rev Genet 2004;5:345–354. doi: 10.1038/nrg1322. pmid:15143317
33. Garber M, Zody MC, Arachchi HM, Berlin A, Gnerre S, Green LM, et al. Closing gaps in the human genome using sequencing by synthesis. Genome Biol. 2009;10:R60. doi: 10.1186/gb-2009-10-6-r60. pmid:19490611
34. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–580. doi: 10.1093/nar/27.2.573. pmid:9862982
35. Butler JM. Genetics and genomics of core short tandem repeat loci used in human identity testing. J Forensic Sci. 2006;51:253–265. doi: 10.1111/j.1556-4029.2006.00046.x. pmid:16566758
36. National Library of Medicine. Basic Local Alignment Search Tool [Internet]. Available: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
37. NET Bio [Internet]. Available: https://github.com/dotnetbio/bio
38. Microsoft takes .NET open source and cross-platform, adds new development capabilities with Visual Studio 2015, .NET 2015 and Visual Studio Online [Internet]. 2014. Microsoft News Center. Available: http://news.microsoft.com/2014/11/12/microsoft-takes-net-open-source-and-cross-platform-adds-new-development-capabilities-with-visual-studio-2015-net-2015-and-visual-studio-online/
39. Martinez K, Cupitt J. VIPS: a highly tuned image processing software architecture. IEEE International Conference on Image Processing. IEEE. 2005;574–577. doi: 10.1109/ICIP.2005.1530120.
Repository Staff Only: item control page
Download Statistics
Download Statistics