Gene Regulation
Ahab	http://gaspard.bio.nyu.edu/Ahab.html
VISTA	http://www-gsd.lbl.gov/vista/index.shtml
PipMaker	http://pipmaker.bx.psu.edu/pipmaker/
CisReg	http://www.mit.edu/~kreiman/resources/cisregul/user_input.html
concise scanner	http://trafac.cchmc.org/trafac/
ConSite	http://mordor.cgb.ki.se/cgi-bin/CONSITE/consite
CREME	http://www.icsi.berkeley.edu/~roded/creme.html
doop	http://doop.abc.hu
gene regulation	http://gene-regulation.com/pub/programs.html
LAGAN	http://lagan.stanford.edu/lagan_web/index.shtml
motive sampler	http://homes.esat.kuleuven.be/~thijs/Work/MotifSampler.html
MSCAN	http://tfscan.cgb.ki.se/cgi-bin/MSCAN
nsite	http://www.softberry.com/berry.phtml?topic=nsite&group=programs&subgroup=promoter
nsitem	http://www.softberry.com/berry.phtml?topic=nsitem&group=programs&subgroup=promoter
opossum	http://www.cisreg.ca/oPOSSUM/
orca	http://burgundy.cmmt.ubc.ca/cgi-bin/OrcaTK/orcatk
Oregano	http://www.oreganno.org/oregano/Index.jsp
OTFBS	http://www.bioinfo.tsinghua.edu.cn/~zhengjsh/OTFBS/
PAP	http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do
Patch	http://www.gene-regulation.com/pub/programs.html#patch
plantcare	http://bioinformatics.psb.ugent.be/webtools/plantcare/html/search_CARE.html
Pmatch	http://www.gene-regulation.com/pub/programs.html#pmatch
pobo	http://www.bioinfo.biocenter.helsinki.fi/poxo
premod	http://genomequebec.mcgill.ca/PReMod/welcome.do;jsessionid=C0A051D4F47558387F3CA5DBEA34EE79
promo	http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3
RSAT	http://rsat.ulb.ac.be/rsat/
rVISTA	http://rvista.dcode.org/
SeqVista	http://zlab.bu.edu/SeqVISTA/
sesimcmc	http://favorov.imb.ac.ru/SeSiMCMC/
Sitecon	http://wwwmgs.bionet.nsc.ru/cgi-bin/mgs/sitecon/sitecon.pl?stage=0
Tfbind	http://tfbind.ims.u-tokyo.ac.jp/
TFBScluster	http://hscl.cimr.cam.ac.uk/TFBScluster_genome_34.html
TFBSfinder	http://cg1.iis.sinica.edu.tw/~TFBSfinder/
Tfsearch	http://www.cbrc.jp/research/db/TFSEARCH.html
tiprod	http://tiprod.cbi.pku.edu.cn:8080/index.html
toucan	http://homes.esat.kuleuven.be/~saerts/software/toucan.php
tractorDB	http://www.bioinfo.cu/Tractor_DB/
trafac	http://trafac.cchmc.org/trafac/index.jsp
TRAFAC	http://trafac.chmcc.org/trafac/index.jsp
transcompel	http://www.gene-regulation.com/pub/databases.html#transcompel
TransFac	http://www.gene-regulation.com/cgi-bin/pub/databases/transfac/search.cgi
transpath	http://www.gene-regulation.com/cgi-bin/pub/databases/transpath/search.cgi
transplorer	http://www.biobase.de/pages/guided_tours/transplorer/transplorer_tour.html
tred	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home
T-Reg Comparator	http://treg.molgen.mpg.de/cgi-bin/pfm_meme_form.pl
trsDB	http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
utr resource	http://bighost.ba.itb.cnr.it/UTR/
vega ensembl	http://vega.sanger.ac.uk/Multi/blastview
webweedeer	http://www.pesolelab.it/index.php?mod=04_Tools
yebis	http://www-btls.jst.go.jp/cgi-bin/Tools/MotifExtraction/index.cgi