Enterobacteria virulence factor prediction server
Keywords:Virulence prediction, amino acid composition, data mining, classifiers, SMO
The continuous usage of antibiotics has resulted in the increase of multidrug resistance in the bacteria. The drastic increase in the bacterial genome projects has paved a path for the identification of potentially novel virulence-associated factors and their possibility as novel drug targets. Thus in the present study, we have implemented SMO classifiers for the better prediction of proteins based on individual protein sequences amino acid composition (AAC) and the performance of evaluation was checked via threshold dependent parameters such as Sensitivity, Specificity, Accuracy, and Mathew correlation coefficient. The predictions are based on the dataset incorporated in the database of five major virulence factors from six pathogens of Enterobacteriacae.This comprehensive database can serve as a source for the selection of significant virulence factor based on the intellectual Gene ontology terms that play a critical role in the pathogenesis and its surveillance in the host.
 Mulder NJ, Mazandu GK &Rapano HA, â€œUsing Host-Pathogen Functional Interactions for Filtering Potential Drug Targets in Mycobacterium tuberculosisâ€, J. Mycobac. Dis, (2013).https://doi.org/10.7196/SAMJ.5437.
 Warner DF & Mizrahi V, â€œApproaches to target identification and validation for tuberculosis drug discovery: a UCT perspectiveâ€, South African Medical Journal, Vol.102, (2012), pp.457-460.
 Waldvogel FA, â€œInfectious diseases in the 21st century: old challenges and new opportunitiesâ€, Int. J. Infect. Dis., Vol.8, (2004), pp.5â€“12.https://doi.org/10.1016/j.ijid.2003.01.001.
 Weiss RA, â€œVirulence and pathogenesisâ€, Trends in Microbiology, Vol.10, (2002), pp.314â€“317.https://doi.org/10.1016/S0966-842X(02)02391-0.
 Hogan D & Kolter R, â€œWhy are bacteria refractory to antimicrobials?â€ Curr. Opin. Microbiol, Vol.5, (2002), pp.472â€“477.https://doi.org/10.1016/S1369-5274(02)00357-0.
 Byarugaba DK, â€œAntimicrobial resistance in developing countries and responsible risk factorsâ€, Int. J. Antimicrob. Agents, Vol.24, (2004), pp.105â€“110.https://doi.org/10.1016/j.ijantimicag.2004.02.015.
 Docampo R, â€œNew and reemerging infectious diseasesâ€, Emerg. Infect. Dis., (2003), pp.1030â€“ 1033.https://doi.org/10.3201/eid0908.030324.
 Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P & Witten IH, â€œThe WEKA data mining software: an updateâ€, ACM SIGKDD explorations newsletter, Vol.11, No.1, (2009).
 Saha S & Raghava GP, â€œPrediction of continuous Bâ€cell epitopes in an antigen using recurrent neural networkâ€, Proteins: Structure, Function, and Bioinformatics, Vol.65, No.1, (2006).https://doi.org/10.1002/prot.21078.
 Kalita MK, Nandal UK, Pattnaik A, Sivalingam A, Ramasamy G, Kumar M, Raghava GP & Gupta D, â€œCyclinPred: a SVM-based method for predicting cyclin protein sequencesâ€, PloS one., Vol.3, No.7, (2008).https://doi.org/10.1371/journal.pone.0002605.
 Tsai CT, Huang WL, Ho SJ, Shu LS & Ho SY, â€œVirulent-GO: prediction of virulent proteins in bacterial pathogens utilizing gene ontology termsâ€, Development, (2009).
 Matthews BW, â€œComparison of the predicted and observed secondary structure of T4 phage lysozymeâ€, BiochimicaETBiophysica Acta (BBA)-Protein Structure, Vol.405, No.2, (1975), pp.442-451.https://doi.org/10.1016/0005-2795(75)90109-9.
 Morens DM, Folkers GK &Fauci AS, â€œThe challenge of emerging and re-emerging infectious diseasesâ€, Nature, Vol.430, (2004), pp.242â€“249.https://doi.org/10.1038/nature02759.
 Pragash DS, Ragunathan L, Banoo S, Rayapu V & Shaker IA, â€œOccurrence of CTX-M and SHV Genes in ESBL Producing Gram Negative Organisms Causing Pyogenic Infections in a Tertiary Care Hospital in Puducherryâ€, Int J Pharm Bio Sci, Vol.3, No.4, (2012).
 Toth IK, Pritchard L & Birch PR, â€œComparative genomics reveals what makes an enterobacterial plant pathogenâ€, Annu. Rev. Phytopathol., Vol.44, (2006).https://doi.org/10.1146/annurev.phyto.44.070505.143444.
 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT & Harris MA, â€œGene Ontology: tool for the unification of biologyâ€, Nature genetics, Vol.25, No.1, (2000), pp.25-29.https://doi.org/10.1038/75556.
 Apweiler R, Bairoch A & Wu CH, â€œProtein sequence Databasesâ€, Curr. Opin Chem. Biol., Vol.8, (2004), pp.76-80.https://doi.org/10.1016/j.cbpa.2003.12.004.
 Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y &Jin Q, â€œVFDB: a reference database for bacterial virulence factorsâ€, Nucleic Acids Res., Vol.33, (2005).