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Algorithmic Aspects of Bioinformatics / Hans-Joachim Böckenhauer, Dirk Bongartz

Main Author Böckenhauer, Hans-Joachim Coauthor Bongartz, Dirk Country Alemanha. Publication Berlin : Springer, cop. 2007 Description X, 396 p. : il. ; 24 cm Series Natural computing series ISBN 978-3-540-71912-0 CDU 57:681.3 681.3:57
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Holdings
Item type Current location Call number Status Date due Barcode Item holds Course reserves
Monografia Biblioteca Geral da Universidade do Minho
BGUMD 111548 Available 397846

Mestrado em Bioinformática Algoritmos para Análise de Sequências Biológicas 1º semestre

Mestrado em Bioinformática Algoritmos Avançados de Bioinformática 2º semestre

Total holds: 0

Enhanced descriptions from Syndetics:

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. Figures, chapter summaries, detailed derivations, and examples, are provided.

Tit. orig.: Algorithmische Grundlagen der Bioinformatik

Table of contents provided by Syndetics

  • 1 Introduction (p. 1)
  • Part I Introduction and Basic Algorithms
  • 2 Basics of Molecular Biology (p. 7)
  • 2.1 Proteins (p. 7)
  • 2.2 Nucleic Acids (p. 9)
  • 2.3 Hereditary Information and Protein Biosynthesis (p. 12)
  • 2.4 Experimental Techniques (p. 15)
  • 2.4.1 Basic Terms and Methods (p. 15)
  • 2.4.2 Duplication of DNA (p. 15)
  • 2.4.3 Gel Electrophoresis and Direct Sequencing (p. 16)
  • 2.4.4 DNA Chips (p. 19)
  • 2.5 Bibliographic Notes (p. 20)
  • 3 Basic Concepts: Strings, Graphs, and Algorithms (p. 23)
  • 3.1 Strings (p. 23)
  • 3.2 Graphs (p. 25)
  • 3.3 Algorithms and Complexity (p. 28)
  • 3.4 Bibliographic Notes (p. 35)
  • 4 String Algorithms (p. 37)
  • 4.1 The String Matching Problem (p. 37)
  • 4.2 String Matching Automata (p. 39)
  • 4.3 The Boyer-Moore Algorithm (p. 44)
  • 4.4 Suffix Trees (p. 50)
  • 4.5 Further Applications of Suffix Trees (p. 58)
  • 4.5.1 Generalized Suffix Trees and the Substring Problem (p. 58)
  • 4.5.2 Longest Common Substrings (p. 61)
  • 4.5.3 Efficient Computation of Overlaps (p. 63)
  • 4.5.4 Repeats in Strings (p. 66)
  • 4.6 Suffix Arrays (p. 68)
  • 4.7 Summary (p. 77)
  • 4.8 Bibliographic Notes (p. 78)
  • 5 Alignment Methods (p. 81)
  • 5.1 Alignment of Two Strings (p. 82)
  • 5.1.1 Basic Definitions (p. 82)
  • 5.1.2 Global Alignment (p. 84)
  • 5.1.3 Local and Semiglobal Alignment (p. 89)
  • 5.1.4 Generalized Scoring Functions (p. 94)
  • 5.2 Heuristic Methods for Database Search (p. 97)
  • 5.2.1 The FASTA Heuristic (p. 98)
  • 5.2.2 The BLAST Heuristic (p. 99)
  • 5.3 Multiple Alignments (p. 101)
  • 5.3.1 Definition and Scoring of Multiple Alignments (p. 101)
  • 5.3.2 Exact Computation of Multiple Alignments (p. 104)
  • 5.3.3 Combining Pairwise Alignments (p. 109)
  • 5.4 Summary (p. 114)
  • 5.5 Bibliographic Notes (p. 114)
  • Part II DNA Sequencing
  • 6 Introduction and Overview (p. 119)
  • 7 Physical Mapping (p. 123)
  • 7.1 Restriction Site Mapping (p. 123)
  • 7.1.1 The Double Digest Approach (p. 124)
  • 7.1.2 The Partial Digest Approach (p. 131)
  • 7.1.3 Comparison of Methods for Restriction Site Mapping (p. 141)
  • 7.2 Hybridization Mapping (p. 143)
  • 7.2.1 Mapping with Unique Probes (p. 146)
  • 7.2.2 Mapping with Unique Probes and Errors (p. 157)
  • 7.2.3 Mapping with Non-unique Probes (p. 165)
  • 7.3 Summary (p. 166)
  • 7.4 Bibliographic Notes (p. 168)
  • 8 DNA Sequencing (p. 171)
  • 8.1 Shotgun Sequencing (p. 171)
  • 8.1.1 Crucial Points to Be Considered in a Suitable Model (p. 174)
  • 8.1.2 The Shortest Common Superstring Problem (p. 176)
  • 8.1.3 Refined Models for Fragment Assembly (p. 196)
  • 8.2 Sequencing by Hybridization (p. 201)
  • 8.3 Summary (p. 207)
  • 8.4 Bibliographic Notes (p. 208)
  • Part III Analyzing Biological Data
  • 9 Finding Signals in DNA Sequences (p. 213)
  • 9.1 Identical and Similar Substrings (p. 213)
  • 9.2 Tandem Repeats (p. 217)
  • 9.3 Frequent and Infrequent Substrings (p. 223)
  • 9.4 Hidden Markov Models (p. 228)
  • 9.5 Summary (p. 235)
  • 9.6 Bibliographic Notes (p. 235)
  • 10 Genome Rearrangements (p. 237)
  • 10.1 Modeling (p. 237)
  • 10.2 Sorting Undirected Permutations (p. 239)
  • 10.3 Sorting Directed Permutations (p. 247)
  • 10.4 Computing the Syntenic Distance (p. 249)
  • 10.5 Summary (p. 255)
  • 10.6 Bibliographic Notes (p. 255)
  • 11 Phylogenetic Trees (p. 257)
  • 11.1 Ultrametric Distances (p. 258)
  • 11.2 Additive Trees (p. 265)
  • 11.3 Characters with Binary States (p. 268)
  • 11.4 The Parsimony Principle and the Quartet Method (p. 275)
  • 11.5 Summary (p. 283)
  • 11.6 Bibliographic Notes (p. 285)
  • 12 Haplotyping (p. 287)
  • 12.1 Inferring Haplotypes from a Population (p. 288)
  • 12.2 Haplotyping a Single Individual (p. 305)
  • 12.3 Summary (p. 316)
  • 12.4 Bibliographic Notes (p. 316)
  • 13 Molecular Structures (p. 319)
  • 13.1 RNA Secondary Structure Prediction (p. 320)
  • 13.1.1 Minimizing the Free Energy (p. 322)
  • 13.1.2 Stochastic Context-Free Grammars (p. 329)
  • 13.2 Structure-Based Comparison of Biomolecules (p. 337)
  • 13.3 Protein Structure Prediction (p. 349)
  • 13.3.1 De Novo Structure Prediction - The HP Model (p. 352)
  • 13.3.2 Protein Threading (p. 363)
  • 13.4 Summary (p. 369)
  • 13.4.1 RNA Secondary Structure Prediction (p. 369)
  • 13.4.2 Structure-Based Comparison of Biomolecules (p. 371)
  • 13.4.3 Protein Structure Prediction (p. 371)
  • 13.5 Bibliographic Notes (p. 372)
  • 13.5.1 RNA Secondary Structure Prediction (p. 372)
  • 13.5.2 Structure-Based Comparison of Biomolecules (p. 373)
  • 13.5.3 Protein Structure Prediction (p. 374)
  • References (p. 377)
  • Index (p. 389)

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