Sequence Comparison.pdf

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B.8 Recurrent Events and the Renewal Theorem 193 Theorem B.3. (Renewal Theorem) If ∑ i b i = B < ∞, ∑ i f i = 1, and µ = ∑ i if i < +∞, and the greatest common divisor of indices i such that f i ≠ 0 is 1, then as n → ∞. v n → B µ
Appendix C Software Packages for <strong>Sequence</strong> Alignment In this appendix, we compile a list of software packages for pairwise alignment, homology search, and multiple alignment. Table C.1 Software packages for pairwise alignment. Package Name Website ARIADNE [145] http://www.well.ox.ac.uk/ariadne band [43] http://globin.bx.psu.edu/dist/band BLASTZ [177] http://www.bx.psu.edu/miller lab/dist/blastz-2004-12-27.tar.gz GAP3 [93] http://deepc2.psi.iastate.edu/aat/align/align.html MUMmer [119] http://mummer.sourceforge.net robust [40] http://globin.bx.psu.edu/dist/robust PipMaker [178] http://bio.cse.psu.edu/pipmaker SIM [92] http://ca.expasy.org/tools/sim.html SIM4 [73] http://globin.bx.psu.edu/dist/sim4/sim4.tar.gz SSEARCH [180] http://fasta.bioch.virginia.edu/fasta www2/fasta list2.shtml Table C.2 Software packages for homology search. Package Name Website BLAST [7, 8] http://www.ncbi.nlm.nih.gov/blast BLAT [109] http://genome.ucsc.edu/cgi-bin/hgBlat FASTA [161] http://fasta.bioch.virginia.edu/fasta www2/fasta list2.shtml MEGABLAST [215] http://www.ncbi.nlm.nih.gov/blast/megablast.shtml PatternHunter [124, 131] http://www.bioinformaticssolutions.com/products/ph WU-BLAST http://blast.wustl.edu 195
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Computational Biology Editors-in-Ch
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Kun-Mao Chao·Louxin Zhang Sequence
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KMC: To Daddy, Mommy, Pei-Pei and L
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viii Foreword I invite you to study
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x Preface Chapters 2 to 5 form the
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Acknowledgments We are extremely gr
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Contents Foreword .................
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Contents xix Part II. Theory ......
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Chapter 1 Introduction 1.1 Biologic
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1.2 Alignment: A Model for Sequence
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1.2 Alignment: A Model for Sequence
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1.3 Scoring Alignment 7 ( ) k m a k
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1.4 Computing Sequence Alignment 9
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1.5 Multiple Alignment 11 1.5 Multi
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1.8 Bibliographic Notes and Further
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PART I. ALGORITHMS AND TECHNIQUES 1
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18 2 Basic Algorithmic Techniques 2
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20 2 Basic Algorithmic Techniques F
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22 2 Basic Algorithmic Techniques s
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28 2 Basic Algorithmic Techniques P
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30 2 Basic Algorithmic Techniques a
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32 2 Basic Algorithmic Techniques O
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Chapter 3 Pairwise Sequence Alignme
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3.3 Global Alignment 37 3.2 Dot Mat
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3.3 Global Alignment 39 ⎧ ⎨ S[i
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3.3 Global Alignment 41 ( ai b j )
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3.4 Local Alignment 43 ⎧ 0, ⎪
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3.4 Local Alignment 45 Algorithm LO
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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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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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Page 160 and 161: Chapter 8 Scoring Matrices With the
Page 162 and 163: 8.1 The PAM Scoring Matrices 151 AB
Page 164 and 165: 8.2 The BLOSUM Scoring Matrices 153
Page 166 and 167: 8.3 General Form of the Scoring Mat
Page 168 and 169: 8.4 How to Select a Scoring Matrix?
Page 170 and 171: 8.5 Compositional Adjustment of Sco
Page 172 and 173: 8.6 DNA Scoring Matrices 161 This i
Page 174 and 175: 8.7 Gap Cost in Gapped Alignments 1
Page 176 and 177: 8.8 Bibliographic Notes and Further
Page 184 and 185: Appendix A Basic Concepts in Molecu
Page 186 and 187: A.4 The Genomes 175 ondary structur
Page 188 and 189: Appendix B Elementary Probability T
Page 190 and 191: B.3 Major Discrete Distributions 17
Page 192 and 193: B.3 Major Discrete Distributions 18
Page 194 and 195: B.5 Mean, Variance, and Moments 183
Page 196 and 197: B.5 Mean, Variance, and Moments 185
Page 198 and 199: B.6 Relative Entropy of Probability
Page 200 and 201: B.7 Discrete-time Finite Markov Cha
Page 202 and 203: B.8 Recurrent Events and the Renewa
Page 206 and 207: 196 C Software Packages for Sequenc
Page 208 and 209: 198 References 19. Bafna, V. and Pe
Page 210 and 211: 200 References 71. Fitch, W.M. and
Page 212 and 213: 202 References 122. Letunic, I., Co
Page 214 and 215: 204 References 173. Robinson, A.B.
Page 216 and 217: Index O-notation, 18 P-value, 139 a
Page 218: Index 209 heuristic, 85 progressive
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