Gerlach, Wolfgang: Taxonomic classification of metagenomic sequences. 2012
Inhalt
- 1 Introduction
- 1.1 DNA
- 1.2 Metagenomics
- 1.2.1 16S-based PCR Amplification
- 1.2.2 Metagenomic Libraries
- 1.2.3 Function-Based Screening
- 1.2.4 Sequence-Based Screening
- 1.2.5 Shotgun Metagenomics
- 1.2.6 Metatranscriptomics & Metaproteomics
- 1.3 Overview of the Thesis
- 1.4 Acknowledgements
- 2 Methods for Taxonomic Classification of Metagenomic Reads
- 2.1 Composition-based Methods
- 2.1.1 TETRA (2004)
- 2.1.2 PhyloPythia (2007)
- 2.1.3 TACOA (2009)
- 2.1.4 RAIphy (2011)
- 2.1.5 Bayesian Classifiers
- 2.2 Comparison-based Methods
- 3 CARMA2 and CARMA3
- 4 WebCARMA
- 5 Experiments
- 5.1 Evaluation Measures
- 5.2 Metagenomes
- 5.3 Databases
- 5.4 Parameter Settings
- 5.5 Experiment 1: CARMA3BLASTx vs CARMA3HMMER3
- 5.6 Experiment 2: CARMA3 vs SOrtITEMS vs MEGAN
- 5.7 Experiment 3: CARMA3 on 454 Biogas Metagenome
- 5.8 Experiment 4: CARMA3 on Assembled Illumina Data
- 5.9 Experiment 5: Applicability of Short Reads for Taxonomic Classification
- 6 Conclusion and Outlook
- Bibliography
- A Appendix
- A.1 WebCARMA Data Formats
- A.2 Simulated Metagenome
- A.3 Evaluation of CARMA3 on Reads of Different Lengths
- A.4 Overlap of Classifications for Order-Filtered Data Set
- A.5 Overlap of Classifications for Species-Filtered Data Set
- A.6 Overlap of Classifications for Unfiltered Data Set
- A.7 Biogas Plant Microbial Community – Overlap
- A.8 Biogas Plant Microbial Community – Comparative Taxonomic Profile
- A.9 Taxonomic Profile of the Human Gut Microbial Gene Catalogue
- A.10 Applicability of Short Reads for Taxonomic Classification