Choudhuri, Jomuna Veronica: Bioinformatics approaches to large scale genome comparison, including the identification of conserved noncoding regions. 2003
Inhalt
- Contents
- List of Figures
- List of Tables
- Introduction
- The REPuter Software
- Repetitive Sequences in Genomes
- Requirements for Repeat Analysis
- Terminology of Repeats
- The REPuter Family of Programs
- Development of Manifold Applications
- The Biological Meaning of Repeats
- Assembly Check
- Localization of Low Copy Repeats Associated with Human Malformations
- Identification of String Uniqueness
- Matching Complementary DNA or Expressed Sequence Tags onto Genomic Sequences
- Comparison of Gene Structure - Part I
- Limitations
- Summary
- Comparative Genomics
- Adapting REPuter to Comparative Genomics
- GenAlyzer vs REPuter: the Main Differences
- The New Repeat Graph
- More Matching Task and Output Options
- Comparison of Gene Structure - Part II
- Summary
- The Neurologic Mutation Wobbler in Mice
- The Wobbler Genomic Region
- Sequence Analysis of the Wobbler Region
- Conservation in Noncoding Regions
- Summary
- Identification and Analysis of Conserved Noncoding Sequences
- Storage of Sequence Data
- Designing Connosseur in Three Phases
- Cascade of Bioinformatics Tools
- Developing Connosseur
- Part One: Sequence Annotation Pipeline
- Part Two: Sequence Comparison -- Conserved Elements Calculation
- Part Three: Conserved Noncoding Sequences Analysis
- Example Application
- Analysis of the Wobbler Region
- Performance
- Summary
- Discussion
- Bibliography
- Links to Human and Mouse Genome Projects
- Useful Web Sites
- Database Relations