Nonparametric Frequency Detection and Optimal Coding in Molecular Biology
The concept of spectral envelope for analyzing periodicities in categorical-valued time series was introduced in the statistics literature as a computationally simple and general statistical methodology for the harmonic analysis and scaling of non-numeric sequences. One benefit of this technique is that it combines nonparametric statistical analysis with modern computer power to quickly search for diagnostic patterns within long sequences. An interesting area of application is the nucleosome positioning signals and optimal alphabets in long DNA sequences. The examples focus on period lengths in nucleosome signals and optimal alphabets in herpesviruses and we point out some inconsistencies in established gene segments.
KeywordsSpectral Analysis Optimal Scaling Nucleosome Positioning Signals Herpesviruses DNA Sequences
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- Stoffer, D.S., D.E. Tyler, A.J. McDougall, and G.A. Schachtel. (1993b). Spectral analysis of DNA sequences (with discussion). Bulletin of the International Statistical Institute, Bk 1, 345–361; Bk 4, 63–69.Google Scholar
- Tavaré, S. and B.W. Giddings. (1989). Some statistical aspects of the primary structure of nucleotide sequences. In Mathematical Methods for DNA Sequences, M.S. Waterman ed., pp. 117–131, Boca Raton, Florida: CRC Press.Google Scholar
- Viari, A., H. Soldano, and E. Ollivier. A scale-independent signal processing method for sequence analysis. Computer Applications in the Biosciences, 6, 71–80.Google Scholar