Sequence Comparison.pdf

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Contents Foreword .......................................................... Preface ............................................................ vii ix Acknowledgments .................................................. xiii About the Authors .................................................. xv 1 Introduction ................................................... 1 1.1 BiologicalMotivations ...................................... 1 1.2 Alignment: A Model for Sequence Comparison . . . .............. 2 1.2.1 Definition . . . ....................................... 2 1.2.2 AlignmentGraph .................................... 3 1.3 Scoring Alignment . . ....................................... 7 1.4 Computing Sequence Alignment . . ............................ 8 1.4.1 Global Alignment Problem ............................ 9 1.4.2 Local Alignment Problem . ............................ 10 1.5 Multiple Alignment . . ....................................... 11 1.6 What Alignments Are Meaningful? . . . . . . ..................... 12 1.7 OverviewoftheBook....................................... 12 1.8 Bibliographic Notes and Further Reading . ..................... 13 Part I. Algorithms and Techniques ................................... 15 2 Basic Algorithmic Techniques ................................... 17 2.1 AlgorithmsandTheirComplexity............................. 18 2.2 Greedy Algorithms . . ....................................... 18 2.2.1 Huffman Codes . . . . . . ................................ 19 2.3 Divide-and-Conquer Strategies . . . ............................ 21 2.3.1 Mergesort .......................................... 21 2.4 Dynamic Programming . . . . . . ................................ 23 2.4.1 Fibonacci Numbers . . ................................ 24 xvii
xviii Contents 2.4.2 TheMaximum-SumSegmentProblem .................. 25 2.4.3 Longest Increasing Subsequences . ..................... 27 2.4.4 Longest Common Subsequences . . ..................... 29 2.5 Bibliographic Notes and Further Reading . ..................... 32 3 Pairwise Sequence Alignment ................................... 35 3.1 Introduction . . . . ........................................... 36 3.2 DotMatrix ................................................ 37 3.3 Global Alignment . . . ....................................... 37 3.4 Local Alignment ........................................... 42 3.5 Various Scoring Schemes . . . . ................................ 46 3.5.1 Affine Gap Penalties . ................................ 46 3.5.2 Constant Gap Penalties . . . ............................ 48 3.5.3 Restricted Affine Gap Penalties . . . ..................... 48 3.6 Space-Saving Strategies . . . . . ................................ 49 3.7 Other Advanced Topics . . . . . ................................ 54 3.7.1 Constrained Sequence Alignment . . ..................... 54 3.7.2 Similar Sequence Alignment . . . . . . ..................... 56 3.7.3 Suboptimal Alignment . . . . ............................ 57 3.7.4 RobustnessMeasurement ............................. 59 3.8 Bibliographic Notes and Further Reading . ..................... 60 4 Homology Search Tools ......................................... 63 4.1 Finding Exact Word Matches . ................................ 64 4.1.1 HashTables......................................... 64 4.1.2 SuffixTrees......................................... 66 4.1.3 SuffixArrays........................................ 67 4.2 FASTA ................................................... 68 4.3 BLAST................................................... 69 4.3.1 Ungapped BLAST . . . ................................ 69 4.3.2 Gapped BLAST . . . . . ................................ 72 4.3.3 PSI-BLAST......................................... 73 4.4 BLAT .................................................... 74 4.5 PatternHunter.............................................. 75 4.6 Bibliographic Notes and Further Reading . ..................... 78 5 Multiple Sequence Alignment ................................... 81 5.1 Aligning Multiple Sequences . ................................ 81 5.2 Scoring Multiple Sequence Alignment . . . . ..................... 82 5.3 An Exact Method for Aligning Three Sequences . . .............. 84 5.4 ProgressiveAlignment ...................................... 85 5.5 Bibliographic Notes and Further Reading . ..................... 86
Page 2 and 3: Computational Biology Editors-in-Ch
Page 4 and 5: Kun-Mao Chao·Louxin Zhang Sequence
Page 6 and 7: KMC: To Daddy, Mommy, Pei-Pei and L
Page 8 and 9: viii Foreword I invite you to study
Page 10 and 11: x Preface Chapters 2 to 5 form the
Page 12 and 13: Acknowledgments We are extremely gr
Page 16 and 17: Contents xix Part II. Theory ......
Page 18 and 19: Chapter 1 Introduction 1.1 Biologic
Page 20 and 21: 1.2 Alignment: A Model for Sequence
Page 22 and 23: 1.2 Alignment: A Model for Sequence
Page 24 and 25: 1.3 Scoring Alignment 7 ( ) k m a k
Page 26 and 27: 1.4 Computing Sequence Alignment 9
Page 28 and 29: 1.5 Multiple Alignment 11 1.5 Multi
Page 30 and 31: 1.8 Bibliographic Notes and Further
Page 32 and 33: PART I. ALGORITHMS AND TECHNIQUES 1
Page 34 and 35: 18 2 Basic Algorithmic Techniques 2
Page 36 and 37: 20 2 Basic Algorithmic Techniques F
Page 38 and 39: 22 2 Basic Algorithmic Techniques s
Page 44 and 45: 28 2 Basic Algorithmic Techniques P
Page 46 and 47: 30 2 Basic Algorithmic Techniques a
Page 48 and 49: 32 2 Basic Algorithmic Techniques O
Page 50 and 51: Chapter 3 Pairwise Sequence Alignme
Page 52 and 53: 3.3 Global Alignment 37 3.2 Dot Mat
Page 54 and 55: 3.3 Global Alignment 39 ⎧ ⎨ S[i
Page 56 and 57: 3.3 Global Alignment 41 ( ai b j )
Page 58 and 59: 3.4 Local Alignment 43 ⎧ 0, ⎪
Page 60 and 61: 3.4 Local Alignment 45 Algorithm LO
Page 62 and 63: 3.5 Various Scoring Schemes 47 Fig.
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3.6 Space-Saving Strategies 49 Fig.
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3.6 Space-Saving Strategies 51 Algo
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3.6 Space-Saving Strategies 53 scor
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3.7 Other Advanced Topics 55 ning,
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3.7 Other Advanced Topics 57 (0,0).
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3.7 Other Advanced Topics 59 3.7.4
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3.8 Bibliographic Notes and Further
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Chapter 4 Homology Search Tools The
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4.1 Finding Exact Word Matches 65 F
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4.1 Finding Exact Word Matches 67 F
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4.3 BLAST 69 SALSDLHAHKLRVDPVNFKLLS
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4.3 BLAST 71 length w, whereas for
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4.3 BLAST 73 Fig. 4.9 A scenario of
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4.5 PatternHunter 75 BLAT identifie
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4.5 PatternHunter 77 can develop an
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82 5 Multiple Sequence Alignment S
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84 5 Multiple Sequence Alignment S
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86 5 Multiple Sequence Alignment Fi
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88 5 Multiple Sequence Alignment al
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Chapter 6 Anatomy of Spaced Seeds B
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6.2 Basic Formulas on Hit Probabili
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6.3 Distance between Non-Overlappin
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6.4 Asymptotic Analysis of Hit Prob
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6.5 Spaced Seed Selection 111 Count
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6.6 Generalizations of Spaced Seeds
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120 7 Local Alignment Statistics tr
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122 7 Local Alignment Statistics Fi
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124 7 Local Alignment Statistics Le
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126 7 Local Alignment Statistics Be
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128 7 Local Alignment Statistics we
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130 7 Local Alignment Statistics A
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132 7 Local Alignment Statistics pr
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134 7 Local Alignment Statistics wh
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136 7 Local Alignment Statistics Ta
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138 7 Local Alignment Statistics Be
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140 7 Local Alignment Statistics 7.
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144 7 Local Alignment Statistics al
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Chapter 8 Scoring Matrices With the
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8.1 The PAM Scoring Matrices 151 AB
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8.2 The BLOSUM Scoring Matrices 153
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8.3 General Form of the Scoring Mat
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8.4 How to Select a Scoring Matrix?
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8.5 Compositional Adjustment of Sco
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8.6 DNA Scoring Matrices 161 This i
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8.7 Gap Cost in Gapped Alignments 1
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Appendix A Basic Concepts in Molecu
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A.4 The Genomes 175 ondary structur
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Appendix B Elementary Probability T
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B.3 Major Discrete Distributions 17
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B.3 Major Discrete Distributions 18
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B.5 Mean, Variance, and Moments 183
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B.5 Mean, Variance, and Moments 185
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B.6 Relative Entropy of Probability
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B.7 Discrete-time Finite Markov Cha
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B.8 Recurrent Events and the Renewa
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B.8 Recurrent Events and the Renewa
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196 C Software Packages for Sequenc
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198 References 19. Bafna, V. and Pe
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200 References 71. Fitch, W.M. and
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202 References 122. Letunic, I., Co
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204 References 173. Robinson, A.B.
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Index O-notation, 18 P-value, 139 a
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Index 209 heuristic, 85 progressive
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