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Biotools for Comparative Microbial Genomics

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Welcome to the Biotools for Comparative Microbial Genomics

A free Unix platform for comparing genome sequences. This platform is the product af a course and workshop that has been taught for more than 10 years. The platform and aim of the course has been changing significantly but now, with this new platform, it is the hope that the system will become more stable and usefull for the people who are initially taught this way of working.

Biotools for comparative genomics work platform

The purpose of this wiki, is to create an interactive community around the Biotools platform. The set of tools presented on the Biotools setup are only a small fraction of what can be done in comparative genomics and this wiki is intended to give each user the option of expanding it in the way they need.

Download and install

The disc image file can be downloaded from this webpage: http://www.cbs.dtu.dk/staff/dave/CMGtools/

The installation guide is build on the VirtualBox software, which allows the user to run a separate operating system parallel to the existing operating system. VirtualBox is free and comes for both Mac OSX and Windows. [1]

CLS Oslo seminar, June 2012

Title: CMG-Biotools, a platform for Comparative Microbial Genomics Abstract: This seminar will present a free platform for doing comparative microbial genomics (CMG) on genome sequence data. We have developed a stand alone operating system (CMG-biotools) designed for microbiologists with limited knowledge in computational analysis. The system will be introduced, and the different functionalities will be presented using a set of example organisms from the class Negativicutes. The functionalities include download of genomes, basic sequence parameters, basic phylogenetic analysis, proteome comparisons using BLAST and DNA structure analysis. The system is free and comes with a basic introduction to Unix, Wiki documentation page and course-like tutorials. Oslo

Negativicutes example

The system was tested on a example dataset of Negativicutes genomes, publicly available. Negativicutes example

Literature references

References for different programs or algorithms as previously published.


  1. Casali N, Nikolayevskyy V, Balabanova Y, Ignatyeva O, Kontsevaya I, Harris SR, Bentley SD, Parkhill J, Nejentsev S, Hoffner SE, Horstmann RD, Brown T, Drobniewski F: Microevolution of extensively drug-resistant tuberculosis in Russia. Genome research 2012
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  3. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA, Venter JC: The minimal gene complement of Mycoplasma genitalium. Science 1995, 270(5235):397–403
  4. Jensen LJ, Friis C, Ussery DW: Three views of microbial genomes. Research in microbiology 1999, 150(9-10):773–7
  5. Friis C, Jensen LJ, Ussery DW: Visualization of pathogenicity regions in bacteria. Genetica 2000, 108:47–51
  6. Pedersen aG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW: A DNA structural atlas for Escherichia coli. Journal of molecular biology 2000, 299(4):907–30
  7. Snipen L, Almø y T, Ussery DW: Microbial comparative pan-genomics using binomial mixture models. BMC genomics 2009, 10:385
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  9. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJB, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ”pan-genome”. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(39):13950–5
  10. Jensen LJ: Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics 2000, 16(4):326–333
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  12. Lagesen K, Hallin P, Rø dland EA, Staerfeldt HH, rn Rognes T, Ussery DW: RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic acids research 2007, 35(9):3100–3108
  13. Larkin Ma, Blackshields G, Brown NP, Chenna R, McGettigan Pa, McWilliam H, Valentin F, Wallace IM, Wilm a, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England) 2007, 23(21):2947–8
  14. Felsenstein J: CONFIDENCE LIMITS ON PHYLOGENIES AN APPROACH USING THE BOOTSTRAP. Evolution 1985, 39(4):783–791
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  17. Satchwell SC, Drew HR, Travers AA: Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology 1986, 191(4):659–675
  18. Ornstein RL, Rein R, Breen DL, Macelroy RD: An optimized potential function for the calculation of nucleic acid interaction energies. I - Base stacking. Biopolymers 1978, 17(10):2341–2360
  19. Shpigelman ES, Trifonov EN, Bolshoy A: CURVATURE: software for the analysis of curved DNA. Computer applications in the biosciences CABIOS 1993, 9(4):435–440
  20. Bolshoy A, McNamara P, Harrington RE, Trifonov EN: Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proceedings of the National Academy of Sciences of the United States of America 1991, 88(6):2312–2316
  21. Mar ́ın A, Xia X: GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: new substitution models incorporating strand bias. Journal of Theoretical Biology 2008, 253(3):508–513
  22. Altschul SS, Gish W, Miller W, Myers EE, Lipman D, Others: Basic Local Alignment Search Tool. Journal of molecular biology 1990, 215(3):403–410
  23. Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW: Genome Update: proteome comparisons. Microbiology (Reading, England) 2005, 151(Pt 1):1–4
  24. Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW: On the Origins of a Vibrio Species. Microbial Ecology 2010, 59:1–13
  25. Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW: Design of a seven-genome Escherichia coli microarray for comparative genomic profiling. Journal of bacteriology 2006, 188(22):7713–21
  26. Klockgether J, Wuerdemann D, Wiehlmann L, Binnewies TT, Ussery DW, Tuemmler B, Cornelis P: Genome diversity of Pseudomonas aeruginosa 2008.
  27. Lobry JR: Asymmetric substitution patterns in the two DNA strands of bacteria. Molecular biology and evolution 1996, 13(5):660–5
  28. Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW: Origin of replication in circular prokaryotic chromosomes. Environmental microbiology 2006, 8(2):353–61

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