PIPS: Pathogenicity Island Prediction Software

Soares SC, Abreu VAC, Ramos RTJ, Cerdeira L, Silva A, Baumbach J, Trost E, Tauch A, Hirata RJ, Mattos-Guaraldi AL, Miyoshi A, et al. (2012)
PLoS ONE 7(2): e30848.

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Abstract
The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands.
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Soares SC, Abreu VAC, Ramos RTJ, et al. PIPS: Pathogenicity Island Prediction Software. PLoS ONE. 2012;7(2): e30848.
Soares, S. C., Abreu, V. A. C., Ramos, R. T. J., Cerdeira, L., Silva, A., Baumbach, J., Trost, E., et al. (2012). PIPS: Pathogenicity Island Prediction Software. PLoS ONE, 7(2), e30848. doi:10.1371/journal.pone.0030848
Soares, S. C., Abreu, V. A. C., Ramos, R. T. J., Cerdeira, L., Silva, A., Baumbach, J., Trost, E., Tauch, A., Hirata, R. J., Mattos-Guaraldi, A. L., et al. (2012). PIPS: Pathogenicity Island Prediction Software. PLoS ONE 7:e30848.
Soares, S.C., et al., 2012. PIPS: Pathogenicity Island Prediction Software. PLoS ONE, 7(2): e30848.
S.C. Soares, et al., “PIPS: Pathogenicity Island Prediction Software”, PLoS ONE, vol. 7, 2012, : e30848.
Soares, S.C., Abreu, V.A.C., Ramos, R.T.J., Cerdeira, L., Silva, A., Baumbach, J., Trost, E., Tauch, A., Hirata, R.J., Mattos-Guaraldi, A.L., Miyoshi, A., Azevedo, V.: PIPS: Pathogenicity Island Prediction Software. PLoS ONE. 7, : e30848 (2012).
Soares, Siomar C., Abreu, Vinicius A. C., Ramos, Rommel T. J., Cerdeira, Louise, Silva, Artur, Baumbach, Jan, Trost, Eva, Tauch, Andreas, Hirata, Raphael Jr, Mattos-Guaraldi, Ana L., Miyoshi, Anderson, and Azevedo, Vasco. “PIPS: Pathogenicity Island Prediction Software”. PLoS ONE 7.2 (2012): e30848.
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31 Citations in Europe PMC

Data provided by Europe PubMed Central.

A shift in the virulence potential of Corynebacterium pseudotuberculosis biovar ovis after passage in a murine host demonstrated through comparative proteomics.
Silva WM, Dorella FA, Soares SC, Souza GH, Castro TL, Seyffert N, Figueiredo H, Miyoshi A, Le Loir Y, Silva A, Azevedo V., BMC Microbiol. 17(1), 2017
PMID: 28327085
Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense.
Gonzalez-Perez MN, Murcia MI, Parra-Lopez C, Blom J, Tauch A., New Microbes New Infect 14(), 2016
PMID: 27818776
Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California.
Dias LM, Alves JT, Veras AA, Barauna RA, Sa PH, Spier S, Edman JM, Guimaraes LC, Rocha FS, Ramos RT, Azevedo V, Silva A, Carneiro AR., Genome Announc 4(1), 2016
PMID: 26950327
Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout.
Figueiredo HC, Soares SC, Pereira FL, Dorella FA, Carvalho AF, Teixeira JP, Azevedo VA, Leal CA., BMC Genomics 16(), 2015
PMID: 26694728
Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology.
Guimaraes L, Soares S, Trost E, Blom J, Ramos R, Silva A, Barh D, Azevedo V., BMC Genomics 16 Suppl 5(), 2015
PMID: 26041051

51 References

Data provided by Europe PubMed Central.

Multiple functions of l0036 in the regulation of the pathogenicity island of enterohaemorrhagic Escherichia coli O157:H7.
Tsai NP, Wu YC, Chen JW, Wu CF, Tzeng CM, Syu WJ., Biochem. J. 393(Pt 2), 2006
PMID: 16248852

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