Genomic signals of chromosomes and of concatenated reoriented coding regions

Paul Dan A. Cristea

doi:10.1117/12.526917

1 July 2004 Genomic signals of chromosomes and of concatenated reoriented coding regions

Paul Dan A. Cristea

Proceedings Volume 5322, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues II; (2004) https://doi.org/10.1117/12.526917
Event: Biomedical Optics 2004, 2004, San Jose, CA, United States

Abstract

Symbolic nucleotide sequences are converted into digital genomic signals by using a complex representation derived from a tetrahedral vector representation of nucleotides. The study of complex genomic signals using signal processing methods reveals large scale features of chromosomes that would be difficult to grasp by using the statistical and pattern matching methods for the analysis of symbolic genomic sequences. On the other hand, in the context of operating with a large volume of data at various resolutions and visualizing the results to make them available to humans, the problem of data representability becomes critical. A novel mathematical description of data representability, based on the data scattering ratio on a pixel is defined and is applied for several typical cases of standard signals and for genomic signals. It is shown that the variation of genomic data along nucleotide sequences, specifically the cumulated and unwrapped phase, can be visualized adequately as simple graphic lines for low and large scales, while for medium scales (thousands to tens of thousands of base pairs) the statistical descriptions have to be used.

Citation Download Citation

Paul Dan A. Cristea "Genomic signals of chromosomes and of concatenated reoriented coding regions", Proc. SPIE 5322, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues II, (1 July 2004); https://doi.org/10.1117/12.526917

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