Methods for Discovery and Characterization of DNA Sequence Motifs - Bioinformatics: A Swiss Perspective - page 29

A last point worth mentioning is that research on transcription factor
binding sites is increasingly based on physical models of protein-DNA inter-
actions and quantitative affinity data. Protein-binding microarrays
(PBMs) 48 and related technologies 49 allow measurement of thousands of
interaction energies in parallel. The TRAP model, 50 which defines the
quantitative relationship between DNA sequence and PBM signal based
on a weight matrix, provides a theoretical basis for inference of a binding
energy matrix from quantitative affinity data. Likewise, thermodynamic
modeling of the SELEX process led to the proposal of a new mathemati-
cal formula to convert base probabilities from motif discovery into base
pair-protein interaction energies. 51
There is definitely more work to be done in the field of DNA motif
discovery.
References
1. Pribnow D. (1975) Nucleotide sequence of an RNA polymerase binding site at
an early T7 promoter. Proc Natl Acad Sci USA 72 (3): 784-8.
2. Williams C. (1966) Adaptation and Natural Selection: A Critique of Some Current
Evolutionary Thought . Princeton, NJ: Princeton University Press, pp. 10-11.
3. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. (1986) Information content
of binding sites on nucleotide sequences . J Mol Biol 188 (3): 415-31.
4. Dung VV, Giao PM, Chinh NN et al . (1993) A new species of living bovid from
Vietnam . Nature 363 : 443-5.
5. Berg OG, von Hippel PH. (1987) Selection of DNA binding sites by regulatory
proteins. Statistical-mechanical theory and application to operators and promoters.
J Mol Biol 193 (4): 723-50.
6. Selassie CD, Mekapati SB, Verma RP. (2002) QSAR: then and now. Curr Top
Med Chem 2 (12): 1357-79.
7. Stormo GD, Schneider TD, Gold L, Ehrenfeucht A. (1982) Use of the
'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
Nucleic Acids Res 10 (9): 2997-3011.
8. Durbin R, Eddy S, Krogh A, Mitchison G. (1998) Biological Sequence Analysis:
Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge
University Press, pp. 46-79.
9. Sandve GK, Drablos F. (2006) A survey of motif discovery methods in an inte-
grated framework. Biol Direct 1 : 11.
10. Das MK, Dai HK. (2007) A survey of DNA motif finding algorithms. BMC
Bioinformatics 8 (Suppl 7): S21.