Table 4 Tools available using CoBaltDB "post" window

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)