Table 4

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

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.

Blanco and Corominas

Blanco and Corominas BMC Genomics 2012 13:688   doi:10.1186/1471-2164-13-688

Open Data