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.
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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This publication cites the following data publications:

22 Citations in Europe PMC

Data provided by Europe PubMed Central.

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
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Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology.
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PMID: 26041051
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Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets.
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PMID: 25705648
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Label-free proteomic analysis to confirm the predicted proteome of Corynebacterium pseudotuberculosis under nitrosative stress mediated by nitric oxide.
Silva WM, Carvalho RD, Soares SC, Bastos IF, Folador EL, Souza GH, Le Loir Y, Miyoshi A, Silva A, Azevedo V., BMC Genomics 15(), 2014
PMID: 25477071
Fine-tuned characterization of Staphylococcus aureus Newbould 305, a strain associated with mild and chronic mastitis in bovines.
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Value of a newly sequenced bacterial genome.
Barbosa EG, Aburjaile FF, Ramos RT, Carneiro AR, Le Loir Y, Baumbach J, Miyoshi A, Silva A, Azevedo V., World J Biol Chem 5(2), 2014
PMID: 24921006
An overview of the domestication and impact of the Salmonella mobilome.
Mebrhatu MT, Cenens W, Aertsen A., Crit. Rev. Microbiol. 40(1), 2014
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Progression of 'OMICS' methodologies for understanding the pathogenicity of Corynebacterium pseudotuberculosis: the Brazilian experience.
Dorella FA, Gala-Garcia A, Pinto AC, Sarrouh B, Antunes CA, Ribeiro D, Aburjaile FF, Fiaux KK, Guimaraes LC, Seyffert N, El-Aouar RA, Silva R, Hassan SS, Castro TL, Marques WS, Ramos R, Carneiro A, de Sa P, Miyoshi A, Azevedo V, Silva A., Comput Struct Biotechnol J 6(), 2013
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The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains.
Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A, Ali A, Santos AR, Pinto AC, Diniz C, Barbosa EG, Dorella FA, Aburjaile F, Rocha FS, Nascimento KK, Guimaraes LC, Almeida S, Hassan SS, Bakhtiar SM, Pereira UP, Abreu VA, Schneider MP, Miyoshi A, Tauch A, Azevedo V., PLoS ONE 8(1), 2013
PMID: 23342011
Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production.
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PMID: 23201561
Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer.
Ramos RT, Carneiro AR, Soares Sde C, dos Santos AR, Almeida S, Guimaraes L, Figueira F, Barbosa E, Tauch A, Azevedo V, Silva A., Microb Biotechnol 6(2), 2013
PMID: 23199210
Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens.
Busby B, Kristensen DM, Koonin EV., Environ. Microbiol. 15(2), 2013
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Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets.
Ali A, Soares SC, Santos AR, Guimaraes LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V., Gene 508(2), 2012
PMID: 22890137
Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia.
Trost E, Blom J, Soares Sde C, Huang IH, Al-Dilaimi A, Schroder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, Azevedo V, Schneider MP, Silva A, Camello TC, Sabbadini PS, Santos CS, Santos LS, Hirata R Jr, Mattos-Guaraldi AL, Efstratiou A, Schmitt MP, Ton-That H, Tauch A., J. Bacteriol. 194(12), 2012
PMID: 22505676

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