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Table 4 Tools available using CoBaltDB "post" window

From: CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

Program Reference Analytical method CoBaltDB features prediction group(s)
LipPred [133] Naive Bayesian Network LIPO    
PRED-LIPO [58] HMM LIPO   (only Monoderm)  
SPEPLip [134] NN LIPO SEC   
SecretomeP [135] Pattern & NN   ΔSEC_SP   
Signal-3L [136] Multi-modules   SEC   
Signal-CF [137] Multi-modules   SEC   
Signal-Blast [138] BlastP   SEC   
Sigcleave EMBOSS Von Heijne method   SEC   
PRED-SIGNAL [129] HMM   SEC (only Archae)  
Flafind [139] AA features   T3SS Archae + T4SS Bacteria   
T3SS_prediction [110] SVM & NN   T3SS   
EffectiveT3 [111] Machine learning   T3SS   
NtraC Signal Analysis [140] Pattern model   SEC (long SP)   
Philius [141] HMM   SEC αTMB  
(SP)OCTOPUS [142, 143] Blast Homology, NN, HMM   SEC αTMB  
MemBrain [144] Machine learning   SEC αTMB  
DAS [145] Dense Alignment Surface    αTMB  
HMM-TM [146] HMM    αTMB  
SVMtop Server 1.0 [147] SVM    αTMB  
waveTM [149] Hydropathy signals algorithm    αTMB  
PRED-TMR [150] AA features    αTMB  
TMAP [67] AA features    αTMB  
igTM [151] Grammatical Inference    αTMB  
TOPCONS [152] Tools Consensus    αTMB  
TUPS [153] Tools Consensus    αTMB  
ConPred II [154] Tools Consensus    αTMB  
MEMSAT3 [66, 155] NN    αTMB  
SABLE [156] NN    αTMB  
TM-Pro [64, 157] AA features    αTMB  
ProspRef _ Knowledge-based method    αTMB  
PSIPRED [158, 159] NN, PSSM    αTMB  
NPS@ [160] Tools Consensus    αTMB  
SAM-T08 [161] HMM    αTMB  
PORTER [162] NN    αTMB  
TMPred EMBnet Weight-matrices    αTMB  
TMMOD [163] HMM    αTMB  
TopPred II [61] G. von Heijne algorithm    αTMB  
YASPIN [164] Hidden Neural Network    αTMB  
MemType-2L [165] PseudoPSSM, classifier    Membrane Type  
BOMP [84] AA features     βBarrel
TMBETADISC-RBF [87] RBF network, PSSM     βBarrel
TMBETA-NET [117] AA features     βBarrel
PRED-TMBB [85] HMM     βBarrel
ConBBPred [76] Tools Consensus     βBarrel
CW-PRED (submit) [126] HMM   Cell-Wall (only Monoderm)   
ProtCompB SoftBerry Multi-methods Localization    
CELLO [166] SVM Localization    
PSL101 [167] SVM, structure homology Localization    
PSLpred [168] SVM Localization    
GPLoc-neg [169] Basic classifier Localization   (only Diderm)  
GPLoc-pos [170] Basic classifier Localization   (only Monoderm)  
LOCtree [171] SVM Localization    
PSORTb [91] Multi-modules Localization    
SLPS [172] Nearest Neighbor on domain Localization    
Couple-subloc v1.0 Jian Guo AA features Localization    
TBPRED [173] SVM Localization   (only Mycobacterium)  
  1. HMM: Hidden Markov Model, NN: Neural Network, AA: Amino Acid, SVM: Support Vector Machine, PSSM: Position Specific Scoring Matrix, T3SS: Type III Secretion System, RBF: Radial Basis Function