Jakobi, Tobias: Bioinformatic methods for eukaryotic RNA-Seq-based promoter identification. 2014
Inhalt
- Introduction
- Background
- DNA sequencing
- Sanger sequencing
- Assessment of sequencing quality
- Next generation sequencing
- Post next generation sequencing
- Promoter analysis
- The eukaryotic transcription process
- Promoters in industrial biotechnology
- The eukaryotic core promoter
- Methods of transcription start site identification
- Genome sequence assembly
- The sequence assembly problem
- Greedy algorithm based methods
- Overlap graph based methods
- de Bruijn graph based methods
- Prerequisites for nucleotide-level promoter analysis
- Motivation and thesis aims
- Targeted assembly with SATYR
- Introduction
- Principal software design and methods
- Implementation of SATYR
- Results
- Targeted assembly on eukaryotic scale
- TSS identification in the Chinese hamster by RNA sequencing
- Previous approaches
- A dual-library RNA sequencing approach for TSS detection
- Bioinformatics analysis pipeline
- Overview of pipeline modules
- General implementation
- Preprocessing
- Transcription start site identification and annotation
- Promoter analysis
- Results
- Preprocessing
- Identification of transcription start sites
- Annotation of transcription start sites
- Gene Ontology classification of transcription start sites
- KEGG based mapping of genes of transcription start sites
- Insights into the Chinese hamster promoter landscape
- Promoter landscapes of the Chinese hamster
- Analysing Chinese hamster promoters on the gene level
- A successful combination
- Discussion