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Computational analysis of the evolution of non-coding genomic sequences
Table of Contents
Abstract
Acknowledgements
Table of Contents
List of Tables
List of Figures
List of Abbreviation
1 Chapter 1. What Do 1000 Genomes Tell Us About Biased Gene Conversion Theory
1.1 Abstract
1.2 Introduction
1.2.1 Tsunamic wave of genomic data
1.2.2 Identification and characterization of haplotypes
1.2.3 Biased Gene Conversion theory
1.3 Materials and Methods
1.3.1 Identification of haplotypes
1.3.2 Testing Biased Gene Conversion theory
1.4 Results
1.4.1 Haplotype classification
1.4.1.1 HMOX1 haplotypes
1.4.1.2 HMOX2 haplotypes
1.4.1.3 AGT haplotypes
1.4.1.4 ZMAT5 haplotypes
1.4.2 Instances of Biased Gene Conversion
1.5 Conclusions
1.6 Discussions
1.7 Additional files
1.8 References
2 Chapter 2. Critical associations and non-randomness of inhomogeneous genomic compositions at middle-range distance
2.1 Abstract
2.2 Introduction
2.2.1 Unusual DNA conformations
2.2.2 Classification of MRI regions
2.2.3 Properties of MRI regions
2.2.4 Genomic signatures
2.3 Materials and Methods
2.4 Results
2.5 Conclusions
2.6 Discussions
2.7 References
3 Chapter 3. Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence
3.1 Abstract
3.2 Background
3.3 Results
3.3.1 Databases of plant orthologous introns
3.3.2 Conserved intronic regions in dicotyledonous plants
3.3.3 Conserved intronic regions in flowering plants
3.3.4 Conserved intronic regions common for moss and angiosperms
3.3.5 Characterization of tRNA-like plant intronic putative ncRNA
3.3.6 Intronic tRNAs of vertebrates
3.4 Discussions
3.5 Conclusions
3.6 Methods
3.6.1 Databases of plant orthologous introns
3.6.2 Computational analysis of RNA secondary structures
3.6.3 BLAST analysis of conserved plant intronic regions
3.6.4 Phylogeny of Arabidopsis tRNAs with CPIR-1 sequence
3.6.5 Mapping gene functions from Gene Ontology database
3.6.6 Computation of intronic tRNAs in humans and mouse
3.6.7 Plant growth conditions and RNA analysis
3.6.8 Northern blot experiments
3.7 Competing interests
3.8 Authors’ contributions
3.9 Acknowledgements
3.10 Figures
3.11 References
3.12 Additional files
A. Appendix A
B. Appendix BBài viết liên quan
