Biotools for Comparative Microbial Genomics

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. 

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
 * 2) Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269(5223):496–512
 * 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
 * 8) Pilo P, Frey J: Bacillus anthracis: Molecular taxonomy, population genetics, phylogeny and patho-evolution. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2011, 11(6):1218–24
 * 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
 * 11) Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC bioinformatics 2010, 11:119
 * 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
 * 15) Perri`ere G, Gouy M: WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 1996, 78(5):364–9
 * 16) Woese CR, Fox GE: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America 1977, 74(11):5088–90.
 * 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