Husemann, Peter; Tauch, Andreas: Bioinformatic approaches for genome finishing. 2011
Inhalt
- 1 Introduction
- 2 Sequencing Technologies -- Biological Background
- 2.1 DNA -- The Backbone of Life on Earth
- 2.2 Technologies to Assess the Sequence of DNA
- 2.2.1 Traditional: Sanger Sequencing
- 2.2.2 The `Next' Generation: Massively Parallel Sequencing
- 2.2.3 Third Generation: Single Molecule Sequencing
- 2.3 Genome Sequencing
- 3 Efficient Matching of Contigs
- 3.1 Finding Local Similarities
- 3.2 Matching by Filtering with q-Grams
- 3.3 r2cat -- The Related Reference Contig Arrangement Tool
- 4 Advanced Contig Layouting using Multiple Reference Genomes
- 4.1 The Contig Adjacency Graph
- 4.2 Finding a Layout of the Contigs
- 4.3 Enhancements of the Graph Creation
- 4.4 Variations of the Contig Layouting
- 5 Realization of the Software
- 6 Layouting Corynebacteria Contigs
- 6.1 Background and Preparatory Steps
- 6.1.1 Description of the Datasets
- 6.1.2 Determining a Reference Layout
- 6.1.3 Parameter Estimation for the Contig Adjacency Graph
- 6.1.4 Other Software for Contig Layouting
- 6.2 Evaluation on Real Sequencing Data
- 7 Summary and Outlook
- Acknowledgments
- Bibliography