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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.