Genomic signal processing
Genomic signal processing
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DOI：
10.1109/79.939833
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发表时间：
2001-07-01
影响因子：
14.9
通讯作者：
Anastassiou, D
中科院分区：
文献类型：
--
作者：
Anastassiou, D
基因组学是一个高度跨学科的领域，它在医学和农业等不同领域创造了范式转变。人们相信，21世纪的许多重大科学和技术努力将与对目前包括人类在内的许多生物体的基因组测序所揭示的大量信息的处理和解释有关。基因组信息是真正意义上的数字化；它以序列的形式表示，其中每个元素可以是有限数量的实体之一。这些序列，如 DNA 和蛋白质，在数学上用字符串表示，其中每个字符都是字母表中的一个字母。对于 DNA，字母表大小为 4，由字母 A、T、C 和 G 组成；对于蛋白质，相应字母的大小为20。正如参考文献列表所示，生物分子序列分析已经成为计算机科学家、物理学家和数学家的主要研究课题。信号处理领域尚未在该领域产生重大影响的主要原因是因为它处理的是数字序列而不是字符串。然而，如果我们正确地将字符串映射到一个或多个数字序列，那么数字信号处理 (DSP) 就会提供一组新颖且有用的工具来解决高度相关的问题。例如，彩色光谱图以局部纹理的形式直观地提供有关生物分子序列的重要信息，这有助于理解局部性质、结构和功能。此外，正确定义的傅立叶变换的幅度和相位都可用于预测重要特征，例如 DNA 中蛋白质编码区的位置和某些特性。甚至可以使用基于数字滤波的模拟来分析将 DNA 映射到蛋白质的过程以及两种序列的相互依赖性。这些和其他基于 DSP 的方法产生了替代的数学公式，并且可以提供改进的计算技术来解决基因组信息科学和技术中的有用问题。
Genomics is a highly cross-disciplinary field that creates paradigm shifts in such diverse areas as medicine and agriculture. It is believed that many significant scientific and technological endeavors in the 21st century will be related to the processing and interpretation of the vast information that is currently revealed from sequencing the genomes of many living organisms, including humans. Genomic information is digital in a very real sense; it is represented in the form of sequences of which each element can be one out of a finite number of entities. Such sequences, like DNA and proteins, have been mathematically represented by character strings, in which each character is a letter of an alphabet. In the case of DNA, the alphabet is size 4 and consists of the letters A, T, C and G; in the case of proteins, the size of the corresponding alphabet is 20. As the list of references shows, biomolecular sequence analysis has already been a major research topic among computer scientists, physicists, and mathematicians. The main reason that the field of signal processing does not yet have significant impact in the field is because it deals with numerical sequences rather than character strings. However, if we properly map a character string into, one or more numerical sequences, then digital signal processing (DSP) provides a set of novel and useful tools for solving highly relevant problems. For example, in the form of local texture, color spectrograms visually provide significant information about biomolecular sequences which facilitates understanding of local nature, structure, and function. Furthermore, both the magnitude and the phase of properly defined Fourier transforms can be used to predict important features like the location and certain properties of protein coding regions in DNA. Even the process of mapping DNA into proteins and the interdependence of the two kinds of sequences can be analyzed using simulations based on digital filtering. These and other DSP-based approaches result in alternative mathematical formulations and may provide improved computational techniques for the solution of useful problems in genomic information science and technology.