An introduction to bioinformatics algorithms:
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| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Cambridge, Mass. [u. a.]
MIT Press
2004
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| Series: | Computational molecular biology
A Bradford book |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | "A Bradford book." |
| Physical Description: | XVIII, 435 S. Ill., graph. Darst., Kt. |
| ISBN: | 0262101068 |
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MARC
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| 245 | 1 | 0 | |a An introduction to bioinformatics algorithms |c Neil C. Jones ; Pavel A. Pevzner |
| 246 | 1 | 3 | |a Bioinformatics algorithms |
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Record in the Search Index
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Contents
Preface
1 Introduction
2 Algorithms and Complexity
2.1 What Is an Algorithm?
2.2 Biological Algorithms versus Computer Algorithms
2.3 The Change Problem
2.4 Correct versus Incorrect Algorithms
2.5 Recursive Algorithms
2.6 Iterative versus Recursive Algorithms
2.7 Fast versus Slow Algorithms
2.8 Big O Notation
2.9 Algorithm Design Techniques
2.9.1 Exhaustive Search
2.9.2 Branch and Bound Algorithms
2.9.3 Greedy Algorithms
2.9.4 Dynamic Programming
2.9.5 Divide and Conquer Algorithms
2.9.6 Machine Learning
2.9.7 Randomized Algorithms
2.10 Tractable versus Intractable Problems
2.11 Notes
Biobox: Richard Karp
2.12 Problems
3 Molecular Biology Primer 57
3.1 What Is Life Made Of? 57
3.2 What Is the Genetic Material? 59
3.3 What Do Genes Do? 60
3.4 What Molecule Codes for Genes? 61
3.5 What Is the Structure of DNA? 61
3.6 What Carries Information between DNA and Proteins? 63
3.7 How Are Proteins Made? 65
3.8 How Can We Analyze DNA? 67
3.8.1 Copying DNA 67
3.8.2 Cutting and Pasting DNA 71
3.8.3 Measuring DNA Length 72
3.8.4 Probing DNA 72
3.9 How Do Individuais of a Species Differ? 73
3.10 How Do Different Species Differ? 74
3.11 Why Bioinformatics? 75
Biobox: Russell Doolittle 79
4 Exhaustive Search 83
4.1 Restriction Mapping 83
4.2 Impractical Restriction Mapping Algorithms 87
4.3 A Practical Restriction Mapping Algorithm 89
4.4 Regulatory Motifs in DNA Sequences 91
4.5 Profiles 93
4.6 The Motif Finding Problem 97
4.7 Search Trees 100
4.8 Finding Motifs 108
4.9 Finding a Mediän String 111
4.10 Notes 114
Biobox: Gary Stormo 116
4.11 Problems 119
5 Greedy Algorithms 125
5.1 Genome Rearrangements 125
5.2 Sorting by Reversais 127
5.3 Approximation Algorithms 131
5.4 Breakpoints: A Different Face of Greed 132
5.5 A Greedy Approach to Motif Finding 136
5.6 Notes 137
Biobox: David Sankoff
5.7 Problems
6 Dynamic Programming Algorithms
6.1 The Power of DNA Sequence Comparison
6.2 The Change Problem Revisited
6.3 The Manhattan Tourist Problem
6.4 Edit Distance and Alignments
6.5 Longest Common Subsequences
6.6 Global Sequence Alignment
6.7 Scoring Alignments
6.8 Local Sequence Alignment
6.9 Alignment with Gap Penalties
6.10 Multiple Alignment
6.11 Gene Prediction
6.12 Statistical Approaches to Gene Prediction
6.13 Similarity Based Approaches to Gene Prediction
6.14 Spliced Alignment
6.15 Notes
Biobox: Michael Waterman
6.16 Problems
7 Divide and Conquer Algorithms
7.1 Divide and Conquer Approach to Sorting
7.2 Space Efficient Sequence Alignment
7.3 Block Alignment and the Four Russians Speedup
7.4 Constructing Alignments in Subquadratic Time
7.5 Notes
Biobox: Webb Miller
7.6 Problems
8 Graph Algorithms
8.1 Graphs
8.2 Graphs and Genetics
8.3 DNA Sequencing
8.4 Shortest Superstring Problem
8.5 DNA Arrays as an Alternative Sequencing Technique
8.6 Sequencing by Hybridization
8.7 SBH as a Hamiltonian Path Problem
xü Contents
8.8 SBH as an Eulerian Path Problem 272
8.9 Fragment Assembly in DNA Sequencing 275
8.10 Protein Sequencing and Identification 280
8.11 The Peptide Sequencing Problem 284
8.12 Spectrum Graphs 287
8.13 Protein Identification via Database Search 290
8.14 Spectral Convolution 292
8.15 Spectral Alignment 293
8.16 Notes 299
8.17 Problems 302
9 Combinatorial Pattern Matching 311
9.1 Repeat Finding 311
9.2 Hash Tables 313
9.3 Exact Pattern Matching 316
9.4 Keyword Trees 318
9.5 Suffix Trees 320
9.6 Heuristic Similarity Search Algorithms 324
9.7 Approximate Pattern Matching 326
9.8 BLAST: Comparing a Sequence against a Database 330
9.9 Notes 331
Biobox: Gene Myers 333
9.10 Problems 337
10 Clustering and Trees 339
10.1 Gene Expression Analysis 339
10.2 Hierarchical Clustering 343
10.3 fc Means Clustering 346
10.4 Clustering and Corrupted Cliques 348
10.5 Evolutionary Trees 354
10.6 Distance Based Tree Reconstruction 358
10.7 Reconstructing Trees from Additive Matrices 361
10.8 Evolutionary Trees and Hierarchical Clustering 366
10.9 Character Based Tree Reconstruction 368
10.10 Small Parsimony Problem 370
10.11 Large Parsimony Problem 374
10.12 Notes 379
Biobox: Ron Shamir 380
10.13 Problems 384
Contents xiii
11 Hidden Markov Models 387
11.1 CG Islands and the "Fair Bet Casino" 387
11.2 The Fair Bet Casino and Hidden Markov Models 390
11.3 Decoding Algorithm 393
11.4 HMM Parameter Estimation 397
11.5 Profile HMM Alignment 398
11.6 Notes 400
Biobox: David Haussler 403
11.7 Problems 407
12 Randomized Algorithms 409
12.1 The Sorting Problem Revisited 409
12.2 Gibbs Sampling 412
12.3 Random Projections 414
12.4 Notes 416
12.5 Problems 417
Using Bioinformatics Tools 419
Bibliography 421
Index 428 |
| any_adam_object | 1 |
| author | Jones, Neil C. Pevzner, Pavel |
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| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 570 - Biology |
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| dewey-tens | 570 - Biology |
| discipline | Biologie Informatik |
| format | Book |
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| institution | BVB |
| isbn | 0262101068 |
| language | English |
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| spelling | Jones, Neil C. Verfasser aut An introduction to bioinformatics algorithms Neil C. Jones ; Pavel A. Pevzner Bioinformatics algorithms Cambridge, Mass. [u. a.] MIT Press 2004 XVIII, 435 S. Ill., graph. Darst., Kt. txt rdacontent n rdamedia nc rdacarrier Computational molecular biology A Bradford book "A Bradford book." Algorithmes Algoritmen gtt Algoritmos genéticos larpcal Bio-informatica gtt Bio-informatique Bioinformática larpcal aBioinformatics aAlgorithms Molekulare Bioinformatik (DE-588)4531334-9 gnd rswk-swf Molekulare Bioinformatik (DE-588)4531334-9 s DE-604 Pevzner, Pavel Verfasser (DE-588)101596737X aut HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=012923189&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Jones, Neil C. Pevzner, Pavel An introduction to bioinformatics algorithms Algorithmes Algoritmen gtt Algoritmos genéticos larpcal Bio-informatica gtt Bio-informatique Bioinformática larpcal aBioinformatics aAlgorithms Molekulare Bioinformatik (DE-588)4531334-9 gnd |
| subject_GND | (DE-588)4531334-9 |
| title | An introduction to bioinformatics algorithms |
| title_alt | Bioinformatics algorithms |
| title_auth | An introduction to bioinformatics algorithms |
| title_exact_search | An introduction to bioinformatics algorithms |
| title_full | An introduction to bioinformatics algorithms Neil C. Jones ; Pavel A. Pevzner |
| title_fullStr | An introduction to bioinformatics algorithms Neil C. Jones ; Pavel A. Pevzner |
| title_full_unstemmed | An introduction to bioinformatics algorithms Neil C. Jones ; Pavel A. Pevzner |
| title_short | An introduction to bioinformatics algorithms |
| title_sort | an introduction to bioinformatics algorithms |
| topic | Algorithmes Algoritmen gtt Algoritmos genéticos larpcal Bio-informatica gtt Bio-informatique Bioinformática larpcal aBioinformatics aAlgorithms Molekulare Bioinformatik (DE-588)4531334-9 gnd |
| topic_facet | Algorithmes Algoritmen Algoritmos genéticos Bio-informatica Bio-informatique Bioinformática aBioinformatics aAlgorithms Molekulare Bioinformatik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=012923189&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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