RNA folding space analysis using structure abstraction:
Saved in:
| Main Author: | |
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| Format: | Thesis Book |
| Language: | English |
| Published: |
2014
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | II, 119 S. Ill., graph. Darst. 30 cm |
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Record in the Search Index
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|---|---|
| adam_text | INAUGURAL-DISSERTATION ZUR ERLANGUNG DER
DOKTORWIIRDE DER FAKULTAT FUR BIOLOGIE DER
ALBERT-LUDWIGS-UNIVERSITAT FREIBURG IM BREISGAU
RNA FOLDING SPACE ANALYSIS USING
STRUCTURE ABSTRACTION
VORGELEGT VON
JIABIN HUANG
GEBOREN IN ZHEJIANG. CHINA
O
U
D
CO
FREIBURG IM BREISGAU
JULI 2014
HTTP://D-NB.INFO/1062548299
CONTENTS
ABSTRACT 1
1. INTRODUCTION 3
1.1. RNA BIOLOGY 3
1.2. RNA STRUCTURES AND FOLDING SPACE 4
1.3. PREDICTING RNA SECONDARY STRUCTURES 7
1.3.1. PREDICTION FOR SINGLE SEQUENCES 7
1.3.2. RNA EVOLUTION AND COMPARATIVE METHODS 8
1.4. FOLDING SPACE ANALYSIS 9
1.5. SUBOPTIMAL FOLDINGS AND SUBENSEMBLES 12
1.5.1. COMPLETE SUBOPTIMAL FOLDING 12
1.5.2. FILTERING 12
1.5.3. SAMPLING AND ABSTRACTION 13
1.6. RNA FOLDING PATHWAY CALCULATION 15
1.7. RNA STRUCTURE COMPARISON 17
1.8. RNA FOLDING KINETICS 19
1.9. ALGEBRAIC DJUAMIC PROGRAMMING 20
2. RESULTS 21
2.1. A POSITION-AWARE STRUCTURE ABSTRACTION 21
2.1.1. FILTERS WITHIN RECURSIVE BACKTRACING 22
2.2. RNA FOLDING PATHWAY CALCULATION 24
2.2.1. HIEAPATH 26
2.2.2. DEMONSTRATION OF PATHWAYS 29
2.3. RNA STRUCTURE COMPARISON 32
2.4. RNA FOLDING KINETICS 32
2.5. FOLDING SPACE ANALYSIS FOR ALIGNMENTS 33
3. DISCUSSION 35
4. MANUSCRIPTS AND PUBLICATIONS 39
4.1. ABSTRACT FOLDING SPACE ANALYSIS BASED ON HELICES 39
4.1.1. OWN WORK 39
4.1.2. PUBLICATION 39
4.2. ANATYSING RNA-KINETICS BASED ON FOLDING SPACE ABSTRACTION 53
4.2.1. OWN WORK 53
CONTENTS
*4.2.2. PUBLICATION 53
4.3. KINETIC ANALYSIS FOR ALIGNMENTS 67
4.3.1. OWN WORK 67
4.3.2. INTRODUCTION 67
4.3.3. MATERIALS AND METHODS 67
4.3.4. RESULTS 70
4.3.5. DISCUSSION 75
A. LOCALLY OPTIMAL FILTERING 79
A.L. HAIRPIN LOOP 81
A.2. BULGE LOOP 83
A.3. INTERNAL LOOP 84
A.4. MULTILOOP 85
A.5. STACKING LOOP 87
A.6. DANGLING ENERGY 88
A.7. SUBSTRUCTURE S 88
B. FOLDING PATHWAYS 91
BIBLIOGRAPHY 99
MANUSCRIPTS AND PUBLICATIONS CONTRIBUTING TO THIS DISSERTATION 109
ABBREVIATIONS 111
LIST OF FIGURES 113
LIST OF TABLES 117
ACKNOWLEDGMENTS 119
II
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| indexdate | 2024-07-10T07:07:49Z |
| institution | BVB |
| language | English |
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| spellingShingle | Huang, Jiabin RNA folding space analysis using structure abstraction |
| subject_GND | (DE-588)4113937-9 |
| title | RNA folding space analysis using structure abstraction |
| title_auth | RNA folding space analysis using structure abstraction |
| title_exact_search | RNA folding space analysis using structure abstraction |
| title_full | RNA folding space analysis using structure abstraction vorgelegt von Jiabin Huang |
| title_fullStr | RNA folding space analysis using structure abstraction vorgelegt von Jiabin Huang |
| title_full_unstemmed | RNA folding space analysis using structure abstraction vorgelegt von Jiabin Huang |
| title_short | RNA folding space analysis using structure abstraction |
| title_sort | rna folding space analysis using structure abstraction |
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