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Table 4 List of the most popular computational tools to characterize gene regulatory regions

From: CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Name

Species

Web Site

Genome Regions

TFs

Comparative Genomics

Chromatin Marks

Graphical Display

Reference

CBS

12 Drosophilas

YES

Full genome

J/T

phastCons

H3K4Me1

UCSC

This work

     

BLAT

H3K4Me3

Gbrowse

 
      

H3K27Ac

  
      

H3K27Me3

  

Chromia

Mouse

YES

Promoters

J/T

NO

H3K4Me1

Own system

[64]

   

Enhancers

  

H3K4Me2

  
      

H3K4Me3

  
      

H3K9Me3

  
      

H3K27Me3

  
      

H3K20Me3

  
      

H3K36Me3

  

CENTIPEDE

Human

NO

Full genome

J/T

PhyloP

H3K4Me1

UCSC

[18]

      

H3K4Me2

  
      

H3K4Me3

  
      

H3K9Ac

  
      

H3K27Ac

  
      

H3K27Me3

  
      

H3K20Me1

  

BLS

12 Drosophilas

NO

Full genome

J/T/ FlyReg

Branch Length Score

NO

NO

[6]

TFMexplorer

Human

YES

Promoters

J/T

NO

NO

Own system

[65]

 

Mouse

       
 

Rat

       
 

Chicken

       
 

Drosophila

       
 

melanogaster

       

DoOPSearch

Multiple

YES

Promoters

-

DoOP

NO

Own system

[66]

 

chordates

       
 

and plants

       

COTRASIF

Multiple

YES

Promoters

J/T

Ensembl

NO

Own system

[67]

 

vertebrates

       
 

and plants

       

Genome surveyor

Drosophila

YES

Full genome

 

Stubb

NO

Gbrowse

[68]

 

melanogaster

       

MAPPER

Human

YES

Promoters

J/T

NO

NO

UCSC

[69]

 

Mouse

       
 

Drosophila

       
 

melanogaster

       

Core_TF

Human

YES

Promoters

T

Ensembl

NO

Own system

[70]

 

Mouse/Rat

       
 

Dog/Chicken

       

Pscan

Human

YES

Promoters

J/T

NO

NO

Own system

[71]

 

Mouse

       
 

Drosophila

       
 

Arabidopsis

       
 

Yeast

       

Contra

Human

YES

Full genome

J/T

phastCons/TBA

NO

Own system

[60]

 

Mouse

       
 

Chicken

       
 

Xenopus

       
 

Zebrafish

       
 

Drosophila

       
 

melanogaster

       
 

Yeast

       

TF-MAP alignments

Trained for vertebrates

YES

Promoters

J/T

Smith & Waterman (maps)

NO

GFF2PS

[47]

   

Enhancers

     

EEL

Trained for vertebrates

NO

Enhancers

J

Smith & Waterman

NO

NO

[72]

RELA

Trained for vertebrates

YES

Promoters

J/T

Smith & Waterman

NO

Own system

[73]

   

Enhancers

     

RSA-tools

Generic

YES

Promoters

-

Multiple approaches

NO

Own system

[29]

   

Enhancers

     

Footprinter

Trained for vertebrates

YES

Promoters

-

Footprinter

NO

Own system

[74]

   

Enhancers

     

Conreal

Trained for vertebrates

YES

Promoters

J/T

CONREAL

NO

Own system

[75]

   

Enhancers

 

LAGAN

   
     

MAVID

   
     

BLASTZ

   

TOUCAN

Trained for vertebrates and plants

YES

Full genome

J/T

Lagan/Avid/ BlastZ/Footprinter

NO

Own system

[76]

  1. For each resource, we studied the following features: name, analyzed genomes, availability of the web server, class of genome sequences, catalogs of predictive models that are incorporated (J for Jaspar and T for Transfac), use of phylogenetical conservation information for evaluation of hits, use of chromatin profiles for reinforcing predictions, and the method selected to display the location of potential hits and reference.
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BMC Genomics

ISSN: 1471-2164

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