Zakrzewski, Martha: Development of computational methods for the analysis of metagenome and metatranscriptome data. 2012
Inhalt
- Introduction
- Background
- State-of-the-art analysis of metagenome data
- Methods for the analysis of 16S rDNA amplicon sequence data
- Methods for the annotation of whole metagenome shotgun data
- Motivation and aims of the thesis
- Methods and implementation
- The novel platform MetaSAMS for the analysis of metagenome data
- Design
- Data model
- Importer
- Tool concept
- The pipeline for the analysis of metagenome reads
- The Pipeline for the analysis of metagenome contigs
- Statistical tools
- Frontend
- The AMPLA pipeline for the analysis of 16S rDNA amplicon sequences
- Processing of raw 16S rDNA amplicon sequences
- Clustering of 16S rDNA amplicon sequences for diversity estimations
- Taxonomic classification of 16S rDNA amplicon sequences
- Phylogenetic characterization of 16S rDNA sequences
- The MeTra pipeline for the characterization of metatranscriptome data
- A method for the identification of industrially relevant enzymes
- Application examples
- Introduction to biogas
- Analysis of a metagenome obtained from a biogas plant by means of MetaSAMS
- Taxonomic profiling of a biogas-producing community
- Functional analysis of processes central in the anaerobic digestion
- Mapping of metagenome reads to the genome of M. marisnigri JR1 via the GenomeMapper
- Identification of variant genes encoding the B subunit of methyl-coenzyme M reductase
- Analysis of 16S rDNA amplicon sequences from a community of a biogas plant
- Processing of raw amplicon sequences obtained from a biogas-producing community
- OTU-based analysis of the biogas-producing community
- Taxonomic profiling of the biogas-producing community based on 16S rDNA amplicon sequences
- Comparative taxonomic analysis of DNA-based profiles created for the biogas-producing community
- Phylogenetic analysis of 16S rDNA amplicon sequences classified as Archaea and Synergistetes
- The metatranscriptome of a biogas-producing microbial community
- Identification of different RNA types in the metatranscriptome data obtained from a biogas fermenter
- Profiling of the transcriptionally active community based on ribosomal sequence tags
- Comparison of the taxonomic profiles obtained by DNA- and RNA-based approaches
- Functional characterizations of mRNA tags identified in the metatranscriptome of the biogas-producing community
- Non-coding RNAs identified in the metatranscriptome of microorganisms residing in a biogas fermenter
- Characterization and identification of laccases
- Discussion
- MetaSAMS - Advantages and limitations
- Challenges in 16S rDNA amplicon sequencing
- Analysis of a metatranscriptome of a biogas-producing community by means of MeTra
- Identification of laccases using hidden Markov models
- Conclusion and outlook
- Bibliography
- Appendix: Laccases in microbial genomes and metagenomes