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Promoter prediction
DNA binding sites: representation and discovery.
G. Stormo.
Bioinformatics, 16:16-23, 2000.
The biology of eukaryotic promoter prediction - a review.
A.G. Pedersen, P.Baldi, Y.Chauvin and S.Brunak.
Computers and chemistry, 23:191-207, 1999.
Identification and functional modelling of DNA sequence elements of
transcription.
T. Werner.
Briefings in bioinformatics, 1:372-380, 2000.
Eukaryotic promoter recognition.
J.W. Fickett and A. G. Hatzigeorgiou.
Genome research, 7:861-878, 1997.
Human-mouse genome comparisons to locate regulatory sites.
W.W. Wasserman, M. Palumbo, W. Thompson, J.W.Fickett and C.E.Lawrence.
Nature genetics, 26:225-228, 2000.
Identification of regulatory regions which confer muscle-specific gene
expression.
W.W. Wasserman and J.W. Fickett.
Journal of molecular biology 278:167-181, 1998.
Searching for regulatory elements in human noncoding region sequences.
L. Duret and P. Bucher.
Current opinion in structural biology, 7:399-406, 1997.
Discovery of patterns
Approaches to the automatic discovery of patterns in biosequences.
A. Brazma, I. Jonassen, I. Eidhammer and D. Gilbert.
Journal of computational biology 5(2): 279-305, 1998.
Detecting subtle sequence signals: a Gibbs sampling strategy for
multiple alignment.
C. E. Lawrence, S. F. Altschul, M. S. Bogusky, J. S. Liu,
A.F. Neuwald and J.C.Wootton.
Science 262: 208-214, 1993.
MatInd and MatInspector: new fast and versatile tools for detection
of consensus matches in nucleotide sequence data.
K. Quandt, K.Frech, H. Karas, E. Wingender and T. Werner.
Nucleic acids research, 23:4878-4884, 1995.
Finding patterns in biological sequences.
B. Brejova, C. Di Marco, T. Vinaf and S. Romero.
Research report, 2000.
(http://monod.uwaterloo.ca/papers/00798gpattern.pdf)
Sequence logos: a new way to display consensus sequences.
T. D. Schneider and R. M. Stephens
Nucleic acids research, 18:6097-6100, 1990.
Databases
The eukaryotic promoter database (EPD).
R.C. Perier, V. Praz, T. Junier, C. Bonnard and P. Bucher.
Nucleic acids research, 28:302-303, 2000.
The TRANSFAC system on gene expression regulation.
E. Wingender et al.
Nucleic acids research, 29:281-283, 2001.
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