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Language(s):
eng - English
Dates:
2008-03-20
Publication Status:
Accepted / In Press
Pages:
IV, 106
Publishing info:
Berlin : Freie Universität Berlin
Table of Contents:
Preface i
1 Introduction 1
1.1 Molecular biology and evolution . . . . . . . . . . . . . . . . . . . . . 1
1.2 Mutational processes . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3 Inferring mutation characteristics . . . . . . . . . . . . . . . . . . . . 10
1.4 Background models of DNA sequences . . . . . . . . . . . . . . . . . 18
1.5 Thesis organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2 DNA insertions and deletions in the human lineage 21
2.1 Identification of indels in the human lineage . . . . . . . . . . . . . . 21
2.2 Tandem duplications and molecular mechanisms . . . . . . . . . . . . 25
2.3 Indels in protein-coding regions . . . . . . . . . . . . . . . . . . . . . 35
3 Tandem duplications and genomic correlations 43
3.1 Dynamical model of sequence evolution . . . . . . . . . . . . . . . . . 44
3.2 Sequence growth and average composition . . . . . . . . . . . . . . . 46
3.3 Stationary two-point correlations . . . . . . . . . . . . . . . . . . . . 49
3.4 Finite-size distribution of the composition bias . . . . . . . . . . . . . 55
3.5 Symmetry breaking and universality . . . . . . . . . . . . . . . . . . 58
3.6 Dynamical correlations . . . . . . . . . . . . . . . . . . . . . . . . . . 62
3.7 General four-letter model and web service CorGen . . . . . . . . . . . 66
3.8 Origin of genomic correlations . . . . . . . . . . . . . . . . . . . . . . 71
4 Genomic correlations and sequence alignment statistics 75
4.1 Sequence alignment and significance assessment . . . . . . . . . . . . 75
4.2 The Gaussian approximation . . . . . . . . . . . . . . . . . . . . . . . 77
4.3 Numerical results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
4.4 Consequences for genomic alignments . . . . . . . . . . . . . . . . . . 84
5 Summary 87
Bibliography 89
Notation and abbreviations 103
Zusammenfassung 105
Rev. Type:
-
Degree:
PhD
