GIPSy: Genomic island prediction software

Soares SC, Geyik H, Ramos RTJ, de Sá PHCG, Barbosa EGV, Baumbach J, Figueiredo HCP, Miyoshi A, Tauch A, Silva A, Azevedo V (2016)
Journal of Biotechnology 232: 2-11.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Soares, Siomar C.; Geyik, Hakan; Ramos, Rommel T. J.; de Sá, Pablo H. C. G.; Barbosa, Eudes G. V.; Baumbach, Jan; Figueiredo, Henrique C. P.; Miyoshi, Anderson; Tauch, AndreasUniBi; Silva, Artur; Azevedo, Vasco
Abstract / Bemerkung
Bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. Horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (GEIs). GEIs may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (PAIs), metabolic islands (MIs), resistance islands (RIs) and symbiotic islands (SIs). Although many software for the prediction of GEIs exist, they only focus on PAI prediction and present other limitations, such as complicated installation and inconvenient user interfaces. Here, we present GIPSy, the genomic island prediction software, a standalone and user-friendly software for the prediction of GEIs, built on our previously developed pathogenicity island prediction software (PIPS). We also present four application cases in which we crosslink data from literature to PAIs, MIs, RIs and SIs predicted by GIPSy. Briefly, GIPSy correctly predicted the following previously described GEIs: 13 PAIs larger than 30kb in Escherichia coli CFT073; 1 MI for Burkholderia pseudomallei K96243, which seems to be a miscellaneous island; 1 RI of Acinetobacter baumannii AYE, named AbaR1; and, 1 SI of Mesorhizobium loti MAFF303099 presenting a mosaic structure. GIPSy is the first life-style-specific genomic island prediction software to perform analyses of PAIs, MIs, RIs and SIs, opening a door for a better understanding of bacterial genome plasticity and the adaptation to new traits. Copyright 2015 Elsevier B.V. All rights reserved.
Genome plasticity; Genomic islands; Horizontal gene transfer; Metabolic islands; Pathogenicity islands; Resistance islands; Symbiotic islands
Journal of Biotechnology
Page URI


Soares SC, Geyik H, Ramos RTJ, et al. GIPSy: Genomic island prediction software. Journal of Biotechnology. 2016;232:2-11.
Soares, S. C., Geyik, H., Ramos, R. T. J., de Sá, P. H. C. G., Barbosa, E. G. V., Baumbach, J., Figueiredo, H. C. P., et al. (2016). GIPSy: Genomic island prediction software. Journal of Biotechnology, 232, 2-11. doi:10.1016/j.jbiotec.2015.09.008
Soares, Siomar C., Geyik, Hakan, Ramos, Rommel T. J., de Sá, Pablo H. C. G., Barbosa, Eudes G. V., Baumbach, Jan, Figueiredo, Henrique C. P., et al. 2016. “GIPSy: Genomic island prediction software”. Journal of Biotechnology 232: 2-11.
Soares, S. C., Geyik, H., Ramos, R. T. J., de Sá, P. H. C. G., Barbosa, E. G. V., Baumbach, J., Figueiredo, H. C. P., Miyoshi, A., Tauch, A., Silva, A., et al. (2016). GIPSy: Genomic island prediction software. Journal of Biotechnology 232, 2-11.
Soares, S.C., et al., 2016. GIPSy: Genomic island prediction software. Journal of Biotechnology, 232, p 2-11.
S.C. Soares, et al., “GIPSy: Genomic island prediction software”, Journal of Biotechnology, vol. 232, 2016, pp. 2-11.
Soares, S.C., Geyik, H., Ramos, R.T.J., de Sá, P.H.C.G., Barbosa, E.G.V., Baumbach, J., Figueiredo, H.C.P., Miyoshi, A., Tauch, A., Silva, A., Azevedo, V.: GIPSy: Genomic island prediction software. Journal of Biotechnology. 232, 2-11 (2016).
Soares, Siomar C., Geyik, Hakan, Ramos, Rommel T. J., de Sá, Pablo H. C. G., Barbosa, Eudes G. V., Baumbach, Jan, Figueiredo, Henrique C. P., Miyoshi, Anderson, Tauch, Andreas, Silva, Artur, and Azevedo, Vasco. “GIPSy: Genomic island prediction software”. Journal of Biotechnology 232 (2016): 2-11.

16 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Extended Spectrum Beta-Lactamase-Producing Gram-Negative Bacteria Recovered From an Amazonian Lake Near the City of Belém, Brazil.
Freitas DY, Araújo S, Folador ARC, Ramos RTJ, Azevedo JSN, Tacão M, Silva A, Henriques I, Baraúna RA., Front Microbiol 10(), 2019
PMID: 30873145
Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts.
Faoro H, Oliveira WK, Weiss VA, Tadra-Sfeir MZ, Cardoso RL, Balsanelli E, Brusamarello-Santos LCC, Camilios-Neto D, Cruz LM, Raittz RT, Marques ACQ, LiPuma J, Fadel-Picheth CMT, Souza EM, Pedrosa FO., BMC Genomics 20(1), 2019
PMID: 31375067
Putative vaccine candidates and drug targets identified by reverse vaccinology and subtractive genomics approaches to control Haemophilus ducreyi, the causative agent of chancroid.
de Sarom A, Kumar Jaiswal A, Tiwari S, de Castro Oliveira L, Barh D, Azevedo V, Jose Oliveira C, de Castro Soares S., J R Soc Interface 15(142), 2018
PMID: 29792307
Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species.
Santos AS, Ramos RT, Silva A, Hirata R, Mattos-Guaraldi AL, Meyer R, Azevedo V, Felicori L, Pacheco LGC., Funct Integr Genomics 18(5), 2018
PMID: 29752561
Microbial genomic island discovery, visualization and analysis.
Bertelli C, Tilley KE, Brinkman FSL., Brief Bioinform (), 2018
PMID: 29868902
Improved genomic island predictions with IslandPath-DIMOB.
Bertelli C, Brinkman FSL., Bioinformatics 34(13), 2018
PMID: 29905770
Virulent Epidemic Pneumonia in Sheep Caused by the Human Pathogen Acinetobacter baumannii.
Linz B, Mukhtar N, Shabbir MZ, Rivera I, Ivanov YV, Tahir Z, Yaqub T, Harvill ET., Front Microbiol 9(), 2018
PMID: 30459734
Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis.
Viana MVC, Sahm A, Góes Neto A, Figueiredo HCP, Wattam AR, Azevedo V., PLoS One 13(11), 2018
PMID: 30419061
Comparative Analysis of Genomic Island Prediction Tools.
da Silva Filho AC, Raittz RT, Guizelini D, De Pierri CR, Augusto DW, Dos Santos-Weiss ICR, Marchaukoski JN., Front Genet 9(), 2018
PMID: 30631340
Whole-Genome Sequence of a Colombian Acinetobacter baumannii Strain, a Coproducer of OXA-72 and OXA-255-Like Carbapenemases.
Saavedra SY, Prada-Cardozo D, Rincón V, Pérez-Cardona H, Hidalgo AM, González MN, Reguero MT, Valenzuela de Silva EM, Mantilla JR, Falquet L, Barreto-Hernández E, Duarte C., Genome Announc 5(7), 2017
PMID: 28209815
Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo.
Viana MVC, Figueiredo H, Ramos R, Guimarães LC, Pereira FL, Dorella FA, Selim SAK, Salaheldean M, Silva A, Wattam AR, Azevedo V., PLoS One 12(4), 2017
PMID: 28445543
Pathoadaptive Mutations of Escherichia coli K1 in Experimental Neonatal Systemic Infection.
McCarthy AJ, Negus D, Martin P, Pechincha C, Oswald E, Stabler RA, Taylor PW., PLoS One 11(11), 2016
PMID: 27861552

38 References

Daten bereitgestellt von Europe PubMed Central.

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA., BMC Genomics 12(), 2011
PMID: 21824423
On the limits of computational functional genomics for bacterial lifestyle prediction.
Barbosa E, Rottger R, Hauschild AC, Azevedo V, Baumbach J., Brief Funct Genomics 13(5), 2014
PMID: 24855068
Conjugative and mobilizable genomic islands in bacteria: evolution and diversity.
Bellanger X, Payot S, Leblond-Bourget N, Guedon G., FEMS Microbiol. Rev. 38(4), 2014
PMID: 24372381
The genetics of symbiotic nitrogen fixation: comparative genomics of 14 rhizobia strains by resolution of protein clusters.
Black M, Moolhuijzen P, Chapman B, Barrero R, Howieson J, Hungria M, Bellgard M., Genes (Basel) 3(1), 2012
PMID: 24704847
Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion.
Brussow H, Canchaya C, Hardt WD., Microbiol. Mol. Biol. Rev. 68(3), 2004
PMID: 15353570
Toxin genes on pathogenicity islands: impact for microbial evolution.
Dobrindt U, Janke B, Piechaczek K, Nagy G, Ziebuhr W, Fischer G, Schierhorn A, Hecker M, Blum-Oehler G, Hacker J., Int. J. Med. Microbiol. 290(4-5), 2000
PMID: 11111903
Whole genome plasticity in pathogenic bacteria.
Dobrindt U, Hacker J., Curr. Opin. Microbiol. 4(5), 2001
PMID: 11587932
Accelerated Profile HMM Searches.
Eddy SR., PLoS Comput. Biol. 7(10), 2011
PMID: 22039361
The Pfam protein families database.
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19920124
Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates.
Hacker J, Bender L, Ott M, Wingender J, Lund B, Marre R, Goebel W., Microb. Pathog. 8(3), 1990
PMID: 1974320
General rules for optimal codon choice.
Hershberg R, Petrov DA., PLoS Genet. 5(7), 2009
PMID: 19593368
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.
Holden MT, Titball RW, Peacock SJ, Cerdeno-Tarraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebaihia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PC, Parkhill J., Proc. Natl. Acad. Sci. U.S.A. 101(39), 2004
PMID: 15377794
Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis.
Holden MT, Hauser H, Sanders M, Ngo TH, Cherevach I, Cronin A, Goodhead I, Mungall K, Quail MA, Price C, Rabbinowitsch E, Sharp S, Croucher NJ, Chieu TB, Mai NT, Diep TS, Chinh NT, Kehoe M, Leigh JA, Ward PN, Dowson CG, Whatmore AM, Chanter N, Iversen P, Gottschalk M, Slater JD, Smith HE, Spratt BG, Xu J, Ye C, Bentley S, Barrell BG, Schultsz C, Maskell DJ, Parkhill J., PLoS ONE 4(7), 2009
PMID: 19603075
Transfer RNAs and pathogenicity islands.
Hou YM., Trends Biochem. Sci. 24(8), 1999
PMID: 10431171
Integrated genomic island prediction tool (IGIPT)
Jain, Proceedings of the 2008 International Conference on Information Technology (), 2008
Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms.
Johnson BR, Klaenhammer TR., Antonie Van Leeuwenhoek 106(1), 2014
PMID: 24748373
tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18957446
Commonalities and differences among symbiosis islands of three Mesorhizobium loti strains.
Kasai-Maita H, Hirakawa H, Nakamura Y, Kaneko T, Miki K, Maruya J, Okazaki S, Tabata S, Saeki K, Sato S., Microbes Environ. 28(2), 2013
PMID: 23666538
ARDB--Antibiotic Resistance Genes Database.
Liu B, Pop M., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18832362
Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli.
Lloyd AL, Rasko DA, Mobley HL., J. Bacteriol. 189(9), 2007
PMID: 17351047
NodMutDB: a database for genes and mutants involved in symbiosis.
Mao C, Qiu J, Wang C, Charles TC, Sobral BW., Bioinformatics 21(12), 2005
PMID: 15817696
The comprehensive antibiotic resistance database.
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O'Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD., Antimicrob. Agents Chemother. 57(7), 2013
PMID: 23650175
Prokaryote diversity and taxonomy: current status and future challenges.
Oren A., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 359(1444), 2004
PMID: 15253349
Pathogenicity islands in bacterial pathogenesis.
Schmidt H, Hensel M., Clin. Microbiol. Rev. 17(1), 2004
PMID: 14726454
PIPS: pathogenicity island prediction software.
Soares SC, Abreu VA, Ramos RT, Cerdeira L, Silva A, Baumbach J, Trost E, Tauch A, Hirata R Jr, Mattos-Guaraldi AL, Miyoshi A, Azevedo V., PLoS ONE 7(2), 2012
PMID: 22355329
Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment.
Sullivan JT, Patrick HN, Lowther WL, Scott DB, Ronson CW., Proc. Natl. Acad. Sci. U.S.A. 92(19), 1995
PMID: 7568057
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
Burkholderia pseudomallei genome plasticity associated with genomic island variation.
Tumapa S, Holden MT, Vesaratchavest M, Wuthiekanun V, Limmathurotsakul D, Chierakul W, Feil EJ, Currie BJ, Day NP, Nierman WC, Peacock SJ., BMC Genomics 9(), 2008
PMID: 18439288
Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome.
Uchiumi T, Ohwada T, Itakura M, Mitsui H, Nukui N, Dawadi P, Kaneko T, Tabata S, Yokoyama T, Tejima K, Saeki K, Omori H, Hayashi M, Maekawa T, Sriprang R, Murooka Y, Tajima S, Simomura K, Nomura M, Suzuki A, Shimoda Y, Sioya K, Abe M, Minamisawa K., J. Bacteriol. 186(8), 2004
PMID: 15060047
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R., BMC Bioinformatics 7(), 2006
PMID: 16542435
Mechanisms of bacterial pathogenicity.
Wilson JW, Schurr MJ, LeBlanc CL, Ramamurthy R, Buchanan KL, Nickerson CA., Postgrad Med J 78(918), 2002
PMID: 11930024
MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications.
Zhou CE, Smith J, Lam M, Zemla A, Dyer MD, Slezak T., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17090593
Functional characterization of a mucus-specific LPXTG surface adhesin from probiotic Lactobacillus rhamnosus GG.
von Ossowski I, Satokari R, Reunanen J, Lebeer S, De Keersmaecker SC, Vanderleyden J, de Vos WM, Palva A., Appl. Environ. Microbiol. 77(13), 2011
PMID: 21602388

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 26376473
PubMed | Europe PMC

Suchen in

Google Scholar