Table 4.
Tools available using CoBaltDB "post" window
| 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 | |||
| UMDHMM_TMHP | [148] | HMM | 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) | ||
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