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Review
. 2009 Oct;5(10):e1000481.
doi: 10.1371/journal.pcbi.1000481. Epub 2009 Oct 26.

Computational resources in infectious disease: limitations and challenges

Eva C Berglund  1 , Björn Nystedt, Siv G E Andersson
Affiliations
Review

Computational resources in infectious disease: limitations and challenges

Eva C Berglund et al. PLoS Comput Biol. 2009 Oct.
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Evolution of a new infectious disease agent.
(A) Recent evolution of the specialist human pathogen M. ulcerans from the aquatic generalist pathogen M. marinum. (B) Arrangement of the three M. ulcerans plasmid–encoded repeated virulence genes (arrows from left to right: mlsA1 [51 kb], mlsA2 [7.6 kb], mlsB [43 kb]) coding for three polyketide synthases. The loading modules (labeled LM) and the 16 repeated modules depicted in purple (labeled 1–9 for mlsA1 and mlsA2, and 1–7 for mlsB) enable the serial buildup of the backbone carbon chain of the complex immunosuppressive substance mycolactone.
Figure 2
Figure 2. New visualization tools for genome comparisons.
Comparison of the genes in multiple genomes can be represented visually by using a 3D program. Each arrow represents one gene, and the grey shading between genes indicates homology. Red indicates genes that are unique to one genome. The difference between this approach and existing programs is that all genomes can be compared to each other simultaneously, rather than by pairwise comparisons. With multiple genomes, and with zooming, flipping, and selecting options, even this rudimentary 3D program would be of great help in genome analysis.
Figure 3
Figure 3. New methods for analyzing evolution by recombination.
Improved models and visualization tools are needed to analyze recombination. Virulence genes, here exemplified by the acfD gene in the Vibrio cholerae pathogenicity island , often display complex recombination patterns. The aligned acfD genes (arrows) from three V. cholerae strains (M2140, M1567, and M1118) are plotted separately; a line connects each site where the nucleotides in two strains differ from the third strain. Noninformative sites were removed before plotting.
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References

    1. Rappuoli R. From Pasteur to genomics: Progress and challenges in infectious diseases. Nat Med. 2004;10:1177–1185. - PMC - PubMed
    1. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, et al. The genome sequence of the SARS-associated coronavirus. Science. 2003;300:1399–1404. - PubMed
    1. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003;300:1394–1399. - PubMed
    1. Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, et al. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001;413:523–527. - PubMed
    1. Welch RA, Burland V, Plunkett G, 3rd, Redford P, Roesch P, et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A. 2002;99:17020–17024. - PMC - PubMed

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