Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Similarly, in metatranscriptomics and metaproteomics, the RNA and protein sequences of such samples are studied. The analysis of these kinds of data often starts by asking the questions of “who is out there?”, “what are they doing?”, and “how do they compare?”. In this chapter, we describe how these computational questions can be addressed using MEGAN, the MEtaGenome ANalyzer program. We first show how to analyze the taxonomic and functional content of a single dataset and then show how such analyses can be performed in a comparative fashion. We demonstrate how to compare different datasets using ecological indices and other distance measures. The discussion is conducted using a number of published marine datasets comprising metagenomic, metatranscriptomic, metaproteomic, and 16S rRNA data.
- What Are the Key Targeted Delivery Technologies of siRNA Now
- Engineering the Caenorhabditis elegans Genome by Mos1-Induced Transgene-Instructed Gene Conversion
- Profiling of Epstein-Barr Virus Latent RNA Expression in Clinical Specimens by Gene-Specific Multiprimed cDNA Synthesis and PCR
- RNAi-Inducing Lentiviral Vectors for Anti-HIV-1 Gene Therapy
- Rapid Directional Walk Within DNA Clones by Step-Out PCR
- Network-Based Analysis of Multivariate Gene Expression Data
- Identify Intronic MicroRNA with Bioinformatics
- Analysis of Recombinational Repair of DNA Double-Strand Breaks in Mammalian Cells With I-SceI Nuclease
- Isolation of Messenger RNA from Plant Tissues
- Mapping Human YAC Clones by Fluorescence In Situ Hybridization Using Alu-PCR from Single Yeast Colonies