Algorithmic Aspects of Bioinformatics

Cover -- Contents -- 1 Introduction -- Part I: Introduction and Basic Algorithms -- 2 Basics of Molecular Biology -- 2.1 Proteins -- 2.2 Nucleic Acids -- 2.3 Hereditary Information and Protein Biosynthesis -- 2.4 Experimental Techniques -- 2.5 Bibliographic Notes -- 3 Basic Concepts: Strings, Graphs, and Algorithms -- 3.1 Strings -- 3.2 Graphs -- 3.3 Algorithms and Complexity -- 3.4 Bibliographic Notes -- 4 String Algorithms -- 4.1 The String Matching Problem -- 4.2 String Matching Automata -- 4.3 The Boyer-Moore Algorithm -- 4.4 Suffix Trees -- 4.5 Further Applications of Suffix Trees -- 4.6 Suffix Arrays -- 4.7 Summary -- 4.8 Bibliographic Notes -- 5 Alignment Methods -- 5.1 Alignment of Two Strings -- 5.2 Heuristic Methods for Database Search -- 5.3 Multiple Alignments -- 5.4 Summary -- 5.5 Bibliographic Notes -- Part II: DNA Sequencing -- 6 Introduction and Overview -- 7 Physical Mapping -- 7.1 Restriction Site Mapping -- 7.2 Hybridization Mapping -- 7.3 Summary -- 7.4 Bibliographic Notes -- 8 DNA Sequencing -- 8.1 Shotgun Sequencing -- 8.2 Sequencing by Hybridization -- 8.3 Summary -- 8.4 Bibliographic Notes -- Part III: Analyzing Biological Data -- 9 Finding Signals in DNA Sequences -- 9.1 Identical and Similar Substrings -- 9.2 Tandem Repeats -- 9.3 Frequent and Infrequent Substrings -- 9.4 Hidden Markov Models -- 9.5 Summary -- 9.6 Bibliographic Notes -- 10 Genome Rearrangements -- 10.1 Modeling -- 10.2 Sorting Undirected Permutations -- 10.3 Sorting Directed Permutations -- 10.4 Computing the Syntenic Distance -- 10.5 Summary -- 10.6 Bibliographic Notes -- 11 Phylogenetic Trees -- 11.1 Ultrametric Distances -- 11.2 Additive Trees -- 11.3 Characters with Binary States -- 11.4 The Parsimony Principle and the Quartet Method -- 11.5 Summary -- 11.6 Bibliographic Notes -- 12 Haplotyping -- 12.1 Inferring Haplotypes from a Population -- 12.2 Haplotyping a Single Individual -- 12.3 Summary -- 12.4 Bibliographic Notes -- 13 Molecular Structures -- 13.1 RNA Secondary Structure Prediction -- 13.2 Structure-Based Comparison of Biomolecules -- 13.3 Protein Structure Prediction -- 13.4 Summary -- 13.5 Bibliographic Notes -- References -- Index -- Last Page.