Table 3

Comparison of GPMiner with several representative gene promoter annotation programs

Transcriptional regulatory features

PromoSer [20]

PromH [49]

DragonGSF [13]

McPromoter [16]

GPMiner


Species supported

Human, mouse, and rat

Human and mouse

Mammalian

Eukaryote

Human, mouse, rat, chimp, and dog

Promoter identification

Yes

Yes

Yes

Yes

Yes

Map to known gene promoters

Yes

-

-

-

DBTSS, EPD and Ensembl

Transcription factor binding site

-

Yes

Yes

-

TRANSFAC public release and JASPAR, MATCH

TATA-box

-

Yes

-

Yes

Yes

Tandem repeat

Yes

-

-

Yes

Tandem Repeat Finder

CpG island

-

-

Yes

-

CpGProD

Over-represented pattern

-

-

-

-

Yes

DNA stability

-

-

-

-

Yes

GC content

-

-

Yes

-

Yes

Co-occurrence of TFBSs

-

Yes

-

-

Yes

Graphical view

Yes

-

-

Yes

Yes


Lee et al. BMC Genomics 2012 13(Suppl 1):S3   doi:10.1186/1471-2164-13-S1-S3

Open Data