Promoters
ALGGEN - RECERCA	http://alggen.lsi.upc.es/recerca/frame-recerca.html
adnan	http://arep.med.harvard.edu/labgc/adnan/hsmmupstream/
TFM suite	http://bioinfo.lifl.fr/TFM/
CARE	http://bioinformatics.psb.ugent.be/webtools/plantcare/html/search_CARE.html
ConTra	http://bioit.dmbr.ugent.be/ConTra/index.php
COTRASIF	http://biomed.org.ua/COTRASIF/
CREME	http://creme.dcode.org/
DBTSS HOME	http://dbtss.hgc.jp/index.html
DiRE	http://dire.dcode.org/
ECR	http://ecrbrowser.dcode.org/
EvoPrinter	http://evoprinter.ninds.nih.gov/
Promoter prediction	http://exon.cshl.org/cgi-bin/atprobe/atprobe.pl
Molby	http://genome.crg.es/cgi-bin/moby/GeneClustering_DataSubmission.cgi
meta WEB server1	http://genome.imim.es/software/meta/demo.html
TF alignment Blanco	http://genome.imim.es/software/meta/meta.html
CompMoby	http://genome.ucsf.edu/compmoby/
PReMod	http://genomequebec.mcgill.ca/PReMod/welcome.do;jsessionid=C0A051D4F47558387F3CA5DBEA34EE79
TOUCAN	http://homes.esat.kuleuven.be/~saerts/software/toucan.php
UTR scan	http://itbtools.ba.itb.cnr.it/utrscan
EMD algorithm	http://kiharalab.org/EMD/
CisFinder	http://lgsun.grc.nia.nih.gov/CisFinder/
CisView Mouse mm6	http://lgsun.grc.nia.nih.gov/cisview/
NIA Mouse Gene Index	http://lgsun.grc.nia.nih.gov/geneindex/mm3/TF.html
cisview	http://lgsun.grc.nia.nih.gov/geneindex/mm6/TFBS/TF_STAT.html
Melina II	http://melina2.hgc.jp/public/index.html
Mulan	http://mulan.dcode.org/
NEI	http://neibank.nei.nih.gov/resources/resources.shtml
BioProspector	http://robotics.stanford.edu/~xsliu/BioProspector/
Regulatory elements	http://rulai.cshl.edu/cgi-bin/regulatory/home.cgi?process=software
CSH Promoter Database	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home
Promoter Database csh	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchPromForm
TF target genes	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm
CREAD	http://rulai.cshl.edu/cread/index.shtml
MatCompare	http://rulai.cshl.edu/MatCompare/
Zhang	http://rulai.cshl.edu/software/index1.htm
Promoter prediction	http://rulai.cshl.org/tools/CpG_promoter/
FirstEF	http://rulai.cshl.org/tools/FirstEF/
CPR	http://rulai.cshl.org/tools/genefinder/CPROMOTER/index.htm
TFBIND	http://tfbind.ims.u-tokyo.ac.jp/
ToppCluster	http://toppcluster.cchmc.org/
TraFaC1	http://trafac.cchmc.org/trafac/ShowFamily;jsessionid=78D46DCAAA61057905372D7AB7224193
TransFind	http://transfind.sys-bio.net/
PASTAA	http://trap.molgen.mpg.de/PASTAA.htm
UTRdb	http://utrdb.ba.itb.cnr.it/
Promoter Analysis - Workbench	http://wiki.c2b2.columbia.edu/workbench/index.php/Promoter_Analysis
FootPrinter 2.0 Web Server	http://wingless.cs.washington.edu/htbin-post/unrestricted/FootPrinterWeb/FootPrinterInput2.pl
Transplorer - Guided Tour	http://www.biobase.de/pages/guided_tours/transplorer/transplorer_tour.html
BioinformaticsOnline.org	http://www.bioinformaticsonline.org/links/ch_09_t_6.html
COGRIM	http://www.cbil.upenn.edu/COGRIM/
TFsearch	http://www.cbrc.jp/research/db/TFSEARCH.html
Promoter 2.0 Prediction Server	http://www.cbs.dtu.dk/services/Promoter/
cisred TF motifs	http://www.cisred.org/
Expander	http://www.cs.tau.ac.il/~rshamir/expander/expander.html
Ensembl Genome Browser	http://www.ensembl.org/index.html
bdgp Neural Network Promoter Prediction	http://www.fruitfly.org/seq_tools/promoter.html
CMA	http://www.gene-regulation.com/cgi-bin/CMA/cma.cgi
TRANSCompeldatabase 7.0	http://www.gene-regulation.com/cgi-bin/pub/databases/transcompel/search.cgi?
TRANSFACdatabase 7.0 - public	http://www.gene-regulation.com/cgi-bin/pub/databases/transfac/search.cgi
TRANSPATH Public	http://www.gene-regulation.com/cgi-bin/pub/databases/transpath/search.cgi
Match	http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi?
Patch	http://www.gene-regulation.com/cgi-bin/pub/programs/patch/bin/patch.cgi
P-Match	http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi
Gene Regulation	http://www.gene-regulation.com/pub/databases.html
biobase	http://www.gene-regulation.com/pub/programs.html
CMA-compsite	http://www.gene-regulation.com/pub/programs/cma/CMA.html
matbase	http://www.genomatix.de/online_help/help_matbase/matbase_help.html
Tfsitescan	http://www.ifti.org/cgi-bin/ifti/Tfsitescan.pl
UCSF Jain Laboratory	http://www.jainlab.org/downloads.html
moduleminer	http://www.kuleuven.be/bioinformatics/
cisregul	http://www.mit.edu/~kreiman/resources/cisregul/user_input.html
MolQuest	http://www.molquest.com/molquest.phtml
ModuleMaster	http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/index.php?excludeReg=1
SoftBerry - index	http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=promoter
Promoter prediction	http://www.softberry.com/berry.phtml?topic=tssg&group=help&subgroup=promoter
Promoters	http://www.softberry.com/berry.phtml?topic=tssw&group=programs&subgroup=promoter
Tanscription Element Listening System	http://www.telis.ucla.edu/
TRRD	http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/
Promoter prediction	http://wwwmgs.bionet.nsc.ru/mgs/programs/proga/