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.