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Special Issues
BioMed Research International
/
2010
/
Article
/
Tab 2
/
Review Article
Emerging Vaccine Informatics
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.