Algorithmic Aspects of Bioinformatics
Description
Advances in bioinformatics and systems biology require improved computational methods for analyzing data, while progress in molecular biology is in turn influencing the development of computer science methods. This book introduces some key problems in bioinformatics, discusses the models used to formally describe these problems, and analyzes the algorithmic approaches used to solve them.
After introducing the basics of molecular biology and algorithmics, Part I explains string algorithms and alignments; Part II details the field of physical mapping and DNA sequencing; and Part III examines the application of algorithmics to the analysis of biological data. Exciting application examples include predicting the spatial structure of proteins, and computing haplotypes from genotype data.
This book describes topics in detail and presents formal models in a mathematically precise, yet intuitive manner, with many figures and chapter summaries, detailed derivations, and examples. It is well suited as an introduction into the field of bioinformatics, and will benefit students and lecturers in bioinformatics and algorithmics, while also offering practitioners an update on current research topics.
Reviews / Votes
From the reviews:
"This book is a worthy leader in what will surely be a torrent of high-level texts inspired by the success of DNA containing genetic instructions. . this book is a highly recommended compendium of applications for geneticists and computer scientists. . The computer science theory is developed in this text with . numerous simple illustrations from DNA." (Harvey Cohn, ACM Computing Reviews, Vol. 49 (12), December, 2008)
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2 Basics of Molecular Biology (p. 7-8)
If one wants to consider questions in the area of molecular biology, as we do in this book, it is an obligatory prerequisite for the development and the evaluation of abstract models and techniques to have at least a basic knowledge about the fundamental principles of molecular biology. We therefore devote this chapter to fundamentals concerning the topics of subsequent chapters, and especially to the classes of biologically most relevant molecules, namely proteins and nucleic acids. The description will be an abstraction and recapitulation of biological knowledge only, and does not claim to be comprehensive or fully detailed. It instead provides an overview of the basic relations in molecular biology serving as a solid background for the problems we are going to consider later in this book. We will thus omit all details that are not necessary for understanding the text.
We start this chapter by the description of proteins in Section 2.1 and nucleic acids in Section 2.2, and their interaction for protein biosynthesis in Section 2.3. Afterwards, we will present some standard techniques used for the analysis of nucleic acids in Section 2.4, and we complete the chapter with some bibliographic notes in Section 2.5.
2.1 Proteins
Proteins represent one of the most important of the molecule classes in living organisms. Their functions include the catalysis of metabolic processes in the form of enzymes, they play an important role in signal transmission, defense mechanisms, and molecule transportation, and they are used as building material, for example in hair.
Proteins are chains of smaller molecular entities, so-called amino acids, which consist of a central carbon atom, denoted as C , connected to an amino group (NH2), a carboxyl group (COOH), and a side chain (R), which is specific for the particular amino acid. The fourth free binding site of C is saturated by a single hydrogen (H) atom. In Figure 2.1, this general structure is shown. According to this, the particular amino acids only di er with respect to their side chains, which also determine their chemical characteristics. We will, however, not consider the detailed chemical structure of the side chains any further.
In nature, there are several known amino acids, but only twenty of them serve as standard building blocks of proteins, these are given in Table 2.1. Next to the names of the amino acid, the corresponding abbreviation and the so-called one letter code is shown. Furthermore, we refer to the polarity of the amino acids, i.e., to their affinity to water, which will play an important role in Section 13.3.
