Integrative analysis if environmental sequences

Update: 2011-06-27

Description

In metagenomics, the aim is to understand the composition and operation of complex microbial assemblages in environmental samples through sequencing and analysis of their DNA. Similarly, metatranscriptomics and metaproteomics target the RNA and proteins obtained from such samples. A major challenge in the analysis of environmental sequences is data integration. The question is how to anaylze different types of data in a unified approach, addressing both taxonomic and functional aspects. We will discuss how to perform taxonomic analysis based on the NCBI taxonomy. Functional analysis can be based on classifications such as the SEED classification of functional roles and subsystems or the KEGG classification of pathways and enzymes. We will also discuss how to compare different datasets using statistical approaches, ecological indices and methods such as Neighbor-net and multi-dimensional scaling.

Comments

In Channel

Estimating ultra-large phylogenies and alignments

2011-06-2856:13

The combinatorics of distance-based tree inference

2011-06-2817:50

Assessing the limits of phylogenomics: can too much data be a bad thing?

2011-06-2701:04:29

Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions

2011-06-2720:34

Integrative analysis if environmental sequences

2011-06-2701:00:47

Mammalian phylogeny reveals recent diversi cation rate shifts

2011-06-2725:01

A generalization of Stirling numbers and distribution of phylogenetic trees

2011-06-2717:17

A Lie algebraic classification of continuous-time Markov models

2011-06-2722:34

Tree reconciliations: beyond the LCA mapping

2011-06-2719:06

Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood

2011-06-2717:54

Speciation & Extinction Rate Estimation from Phylogenetic Trees

2011-06-2722:15

Trees as representations of evolutionary information worth keeping

2011-06-2759:54

Are there alternatives to handling site-to-site rate variation in evolutionary characters

2011-06-2701:06:53

An empirical study of the effect of sequence alignment on phylogenetic analysis

2011-06-2720:41

Modelling protein evolution

2011-06-2757:39

Sequence Classification using Reference Taxonomies

2011-06-2401:03:44

Evaluating the goodness of fit between a phylogenetic model and an alignment

2011-06-2457:49

Phylodynamic inference - accounting for the interaction of evolutionary and ecological processes

2011-06-2415:40

Genome sequencing of Leishmania donovani clinical lines reveals dynamic phylogenetic variation

2011-06-2421:10

New methods of identifying fast-evolving sites in aligned sequence data

2011-06-2424:42

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Integrative analysis if environmental sequences

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Integrative analysis if environmental sequences

Steve Greenham

Integrative analysis if environmental sequences