Table 2: Tools used for reverse vaccinology.

Tool nameWebsite URLCommentRefs

ORF prediction and genome annotation
 GLIMMERhttp://www.cbcb.umd.edu/software/glimmer/Interpolated Markov models[85]
 ORPHEUShttp://pedant.gsf.de/orpheus/ (not working now)Codon usage and ribosome binding statistics[86]
 GeneMarkhttp://exon.gatech.edu/GeneMark/HMM[87]

Bacterial protein localization prediction
 PSORTbhttp://www.psort.org/psortb/Multicomponent[97]
 Proteome Analysthttp://webdocs.cs.ualberta.ca/~bioinfo/PA/Sub/Annotation keywords[99]
 SubLochttp://www.bioinfo.tsinghua.edu.cn/SubLoc/SVM[257]
 CELLOhttp://cello.life.nctu.edu.tw/SVM[98]
 PSLpredhttp://www.imtech.res.in/raghava/pslpred/SVM[258]
 LOCtreehttp://cubic.bioc.columbia.edu/cgi/var/nair/loctree/querySVM[259]
 SignalPhttp://www.cbs.dtu.dk/services/SignalP/NN, HMM[260]

Sequence conservation
 BLASThttp://blast.ncbi.nlm.nih.gov/Best reciprocal BLAST hit[261]
 OrthoMCLhttp://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgiSVM[262]

Transmembrane domain prediction
 HMMTOPhttp://www.enzim.hu/hmmtop/HMM[263]
 PRED-TMBBhttp://biophysics.biol.uoa.gr/PRED-TMBB/HMM (β-barrel)[264]
 TBBpredhttp://www.imtech.res.in/raghava/tbbpred/NN, SVM (β-barrel)[265]
 PROFtmbhttp://cubic.bioc.columbia.edu/services/proftmb/HMM[266]

Bacterial adhesin prediction
 SPAANftp://203.195.151.45NN[112]

Reverse vaccinology software
 NERVEhttp://www.bio.unipd.it/molbinfo/ReverseVaccinology_NERVE.htmlMulticomponent[113]
 Vaxignhttp://www.violinet.org/vaxign/Web-based, multicomponent[110]

Abbreviations: HMM: hidden Markov model; NN: neuron network; SVM: support vector machine.