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.