Table 2.

Tools used for reverse vaccinology.

Tool name	Website URL	Comment	Refs
ORF prediction and genome annotation
GLIMMER	http://www.cbcb.umd.edu/software/glimmer/	Interpolated Markov models	[85]
ORPHEUS	http://pedant.gsf.de/orpheus/ (not working now)	Codon usage and ribosome binding statistics	[86]
GeneMark	http://exon.gatech.edu/GeneMark/	HMM	[87]
Bacterial protein localization prediction
PSORTb	http://www.psort.org/psortb/	Multicomponent	[97]
Proteome Analyst	http://webdocs.cs.ualberta.ca/~bioinfo/PA/Sub/	Annotation keywords	[99]
SubLoc	http://www.bioinfo.tsinghua.edu.cn/SubLoc/	SVM	[257]
CELLO	http://cello.life.nctu.edu.tw/	SVM	[98]
PSLpred	http://www.imtech.res.in/raghava/pslpred/	SVM	[258]
LOCtree	http://cubic.bioc.columbia.edu/cgi/var/nair/loctree/query	SVM	[259]
SignalP	http://www.cbs.dtu.dk/services/SignalP/	NN, HMM	[260]
Sequence conservation
BLAST	http://blast.ncbi.nlm.nih.gov/	Best reciprocal BLAST hit	[261]
OrthoMCL	http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi	SVM	[262]
Transmembrane domain prediction
HMMTOP	http://www.enzim.hu/hmmtop/	HMM	[263]
PRED-TMBB	http://biophysics.biol.uoa.gr/PRED-TMBB/	HMM (β-barrel)	[264]
TBBpred	http://www.imtech.res.in/raghava/tbbpred/	NN, SVM (β-barrel)	[265]
PROFtmb	http://cubic.bioc.columbia.edu/services/proftmb/	HMM	[266]
Bacterial adhesin prediction
SPAAN	ftp://203.195.151.45	NN	[112]
Reverse vaccinology software
NERVE	http://www.bio.unipd.it/molbinfo/ReverseVaccinology_NERVE.html	Multicomponent	[113]
Vaxign	http://www.violinet.org/vaxign/	Web-based, multicomponent	[110]

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