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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  
Core-Promoter—for finding RNAPII promoters of human genes by quadratic discriminant analysis Zhang (1998a, b)
EPD Eukaryotic promoter database;
Bucher (1990); Périer et al. (1999, 2000)
EpoDB genes expressed during vertebrate erythropoiesis; also links to pancreas and other gene expression databases Stoeckert et al. (1999)
GeneExpress analysis of transcriptional regulations with TRRD database Kolchanov et al. (1999a,b)
Genome inspector for combined analysis of multiple signals in genomes Quandt et al. (1997)
GrailIIb prediction of TSS by neural networks based on scores of characteristic sequence patterns and composition Uberbacher and Mural (1991); Uberbacher et al. (1996)
MAR-FINDER for finding matrix attachment regions Kramer et al. (1997); Singh et al. (1997)
MatInd—see Transfac database    
MatInspector—see Transfac database  
Mirage (Molecular Informatics Resource for the Analysis of Gene Expression) see Web page
NNPP Promoter Prediction by Neural Network for prokaryotes or eukaryotes Reese et al. (1996)
NSITE—search for TF-binding sites or other consensus regulatory sequences
see Web site
Nuclear (including glucocorticoid) receptor resource Martinez et al. (1997)
OOTFD Object-Oriented Transcription Factor Database Ghosh (1998)
PLACE plant cis-acting regulatory elements Higo et al. (1999)
PlantCARE plants cis-acting regulatory elements 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 Tabaska and Zhang (1999)
Promoter element weight matrices and HMMs Bucher (1990)
Promoter II for recognition of PolII sequences by neural networks Knudsen (1999)
PromoterInspector Klingenhoff et al. (1999)
PromoterScanc Prestridge (1995) and see Web site
Sequence walkers for graphical viewing of the interaction of regulatory protein with DNA-binding site
Schneider (1997)
Signal scan for transcriptional elements Prestridge (1991, 1996)
TESS for searching for transcription factor binding–sites Schug and Overton (1997a,b)
Tfbind for transcription factor–binding sites Tsunoda and Takagi (1999)
Thyroid receptor resourced see Web page
Transfac programs providing search for TF-binding sites. MatInd for making scoring matrices and MatInspector for searching for matches to matrices see
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;
see Web site
TSSW; recognition of human PolII promoter region and start of transcription by linear discriminant function analysis;
see Web site
Yeast cell cycle gene retrieval and promoter analysis
Wolfsberg et al. (1999)
Yeast cell cycle analysis project Spellman et al. (1998)
    Multiple methods of analysis are offered at sites and Lists of Web sites are given at and 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
    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.


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