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Table 1 A summary of CoBaltDB precomputed features-tools

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

Program

Reference

Analytical method

CoBaltDB features prediction group(s)

LipoP 1.0 Server

[59]

HMM + NN

LIPO

 

SEC

  

DOLOP

[57]

RE

LIPO

    

LIPO

[56]

RE

LIPO

    

TatP 1.0

[53]

RE + NN

 

TAT

   

TATFIND 1.4

[52]

RE

 

TAT

   

PrediSi

[112]

Position weight matrix

  

SEC

  

SignalP 3.0 Server

[45–47]

HMM + NN

  

SEC

  

SOSUIsignal

[113]

Multi-programs

  

SEC

  

SIG-Pred

J.R. Bradford

Matrix

  

SEC

  

RPSP

[44]

NN

  

SEC

  

Phobius

[48, 49]

HMM

  

SEC

αTMB

 

HMMTOP

[71]

HMM

   

αTMB

 

TMHMM Server v.2.0

[70]

HMM

   

αTMB

 

TM-Finder

[65]

AA FEATURES

   

αTMB

 

SOSUI

[114]

AA FEATURES

   

αTMB

 

SVMtm

[73]

SVM

   

αTMB

 

SPLIT 4.0 Server

[115]

AA FEATURES

   

αTMB

 

MCMBB

[116]

HMM

    

βBarrel

TMBETADISC:

[117]

      

_COMP

 

AA FEATURES

    

βBarrel

_DIPEPTIDE

 

Dipeptide composition

    

βBarrel

_MOTIF

 

Motif(s)

    

βBarrel

TMB-Hunt2

[118]

SVM

    

βBarrel

  1. HMM: Hidden Markov Model, NN: Neural Network, RE: Regular Expression, AA: Amino Acid, SVM: Support Vector Machine