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Table 9.6. Promoter prediction programs, Web pages, and related information
Name		Web address		Reference
BDNA video analysis of transcription factor–binding sites using conformational and physicochemical DNA features	see GeneExpress	Ponomarenko et al. (1999)
ConsInspector—see Transfac databasea	http://www.gsf.de/biodv/consinspector.html
Core-Promoter—for finding RNAPII promoters of human genes by quadratic discriminant analysis	http://rulai.cshl.edu	Zhang (1998a, b)
EPD Eukaryotic promoter database	http://www.epd.isb-sib.ch/; http://www.epd.isb-sib.ch/promoter_elements/	Bucher (1990); Périer et al. (1999, 2000)
EpoDB genes expressed during vertebrate erythropoiesis; also links to pancreas and other gene expression databases	http://www.cbil.upenn.edu/	Stoeckert et al. (1999)
GeneExpress analysis of transcriptional regulations with TRRD database	http://wwwmgs.bionet.nsc.ru/mgs/systems/geneexpress/	Kolchanov et al. (1999a,b)
Genome inspector for combined analysis of multiple signals in genomes	http://www.gsf.de/biodv/genomeinspector.html	Quandt et al. (1997)
GrailIIb prediction of TSS by neural networks based on scores of characteristic sequence patterns and composition	http://compbio.ornl.gov/Grail-1.3/	Uberbacher and Mural (1991); Uberbacher et al. (1996)
MAR-FINDER for finding matrix attachment regions	http://www.futuresoft.org/MAR-Wiz/	Kramer et al. (1997); Singh et al. (1997)
MatInd—see Transfac database
MatInspector—see Transfac database	http://www.genomatix.de/cgi-bin/matinspector/matinspector.pl
Mirage (Molecular Informatics Resource for the Analysis of Gene Expression)	http://www.ifti.org/	see Web page
NNPP Promoter Prediction by Neural Network for prokaryotes or eukaryotes	http://www.fruitfly.org/seq_tools/promoter.html	Reese et al. (1996)
NSITE—search for TF-binding sites or other consensus regulatory sequences	http://www.bioinformatics.vg/biolinks/bioinformatics/ verbose/Promoter%2520Scan.shtml	see Web site
Nuclear (including glucocorticoid) receptor resource	http://nrr.georgetown.edu/NRR/nrrhome.htm	Martinez et al. (1997)
OOTFD Object-Oriented Transcription Factor Database	http://www.ifti.org/cgi-bin/ifti/ootfd.pl	Ghosh (1998)
PLACE plant cis-acting regulatory elements	http://www.dna.affrc.go.jp/htdocs/PLACE/	Higo et al. (1999)
PlantCARE plants cis-acting regulatory elements	http://oberon.fvms.ugent.be:8080/PlantCARE/	Rombauts et al. (1999)
Pol3scan for RNAP III/tRNA promoter sequences using pattern scoring matrices	perform Web search	Pavesi et al. (1994)
Polyadq for locating polyadenylation sites	http://rulai.cshl.edu	Tabaska and Zhang (1999)
Promoter element weight matrices and HMMs	http://www.epd.isb-sib.ch/promoter_elements/	Bucher (1990)
Promoter II for recognition of PolII sequences by neural networks	http://www.cbs.dtu.dk/services/promoter/	Knudsen (1999)
PromoterInspector	http://www.gsf.de/biodv/	Klingenhoff et al. (1999)
PromoterScanc	http://bimas.dcrt.nih.gov/molbio/proscan/	Prestridge (1995) and see Web site
Sequence walkers for graphical viewing of the interaction of regulatory protein with DNA-binding site	http://www-lecb.ncifcrf.gov/~toms/walker/ narcoverlogowalker.html	Schneider (1997)
Signal scan for transcriptional elements	http://bimas.dcrt.nih.gov:80/molbio/signal/	Prestridge (1991, 1996)
TESS for searching for transcription factor binding–sites	http://www.cbil.upenn.edu/tess/	Schug and Overton (1997a,b)
Tfbind for transcription factor–binding sites	http://tfbind.ims.u-tokyo.ac.jp	Tsunoda and Takagi (1999)
Thyroid receptor resourced	http://xanadu.mgh.harvard.edu/receptor/trrfront.html	see Web page
Transfac programs providing search for TF-binding sites. MatInd for making scoring matrices and MatInspector for searching for matches to matrices	http://www.genomatix.de/cgi-bin/matinspector/matinspector.pl	see http://www.gsf.de/biodv/ staff_pub.html; Knüppel et al. (1994); Quandt et al. (1995); Heinemeyer et al. (1999); Klingenhoff et al. (1999)
TRRD transcriptional regulatory region database; see GeneExpress		Kolchanov et al. (1999a)
TSSG, like TSSW but based on sequences from a different promoter database	http://genomic.sanger.ac.uk/gf/gf.shtml; http://searchlauncher.bcm.tmc.edu/ seq-search/gene-search.html	see Web site
TSSW; recognition of human PolII promoter region and start of transcription by linear discriminant function analysis	http://genomic.sanger.ac.uk/gf/gf.shtml; http://searchlauncher.bcm.tmc.edu/ seq-search/gene-search.html	see Web site
Yeast cell cycle gene retrieval and promoter analysis	http://www.ncbi.nlm.nih.gov/CBBresearch/ Landsman/Cell_cycle_data/upstream_seq.html; http://www.ncbi.nlm.nih.gov/CBBresearch/ Landsman/Cell_cycle_data/	Wolfsberg et al. (1999)
Yeast cell cycle analysis project	http://genome-www.stanford.edu/cellcycle/info	Spellman et al. (1998)
Multiple methods of analysis are offered at sites http://searchlauncher.bcm.tmc.edu/seq-search/gene-search.html and http://genomic.sanger.ac.uk/gf/gf.shtml. Lists of Web sites are given at http://linkage.rockefeller.edu/soft/linkage/ and http://biobenchelper.hypermart.net/index.html. A comparison of many of the promoter prediction programs included in this table and several additional ones on a small number of promoter-containing sequences not used in program training is available (Fickett and Hatzigeorgiou 1997).     a MatInspector DOS, Windows 95 and NT, and Mac versions and ConsInspector DOS and Mac versions available by FTP from ariane.gsf.de/pub/.     b GrailII must be given both gene and promoter sequences.     c Accepts one person at a time; DOS version also available.     d Includes links to other receptor databases.