Ander, Christina: Bioinformatic methods for the analysis and comparison of metagenomes and metatranscriptomes. 2014
Inhalt
- 1 Introduction
- 1.1 Research on microbial communities
- 1.1.1 Central biological dogma
- 1.1.2 DNA Sequencing
- 1.1.3 History of metagenomics
- 1.1.4 Research techniques for non culturable microorganisms
- 1.1.5 Bioinformatic challenges in modern microbial research
- 1.2 Overview of this thesis
- 2 metaBEETL - A taxonomic classifier
- 2.1 Introduction to taxonomic classification of microbial communities
- 2.1.1 Targeted gene metagenomics
- 2.1.2 Whole genome metagenomics
- 2.1.3 Taxonomic classification methods
- 2.2 Algorithmic background
- 2.3 metaBEETL - Taxonomic classification of whole genome metagenomic sequences
- 2.4 Accuracy tests of metaBEETL
- 2.4.1 Reference database
- 2.4.2 Accuracy test on a simulated metagenome
- 2.4.3 metaBEETL accuracy test on a modified database
- 2.5 Discussion of metaBEETL
- 3 Metrans - a software platform for the analysis of metatranscriptomes
- 3.1 Transcription analysis
- 3.2 Metrans - analysis pipeline and software structure
- 3.2.1 Metrans analysis pipeline
- 3.2.2 Data storage and operating system
- 3.2.3 Software architecture
- 3.2.4 Graphical user interface
- 3.3 Application example
- 3.4 Conclusion
- 4 Conclusion and outlook
- Bibliography
- A metaBEETL