Introduction

Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.

Publications

  1. Phylogenetic classification of short environmental DNA fragments.
    Cite this
    Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J, 2008-04-01 - Nucleic acids research

Credits

  1. Lutz Krause
    Developer

  2. Naryttza N Diaz
    Developer

  3. Alexander Goesmann
    Developer

  4. Scott Kelley
    Developer

  5. Tim W Nattkemper
    Developer

  6. Forest Rohwer
    Developer

  7. Robert A Edwards
    Developer

  8. Jens Stoye
    Investigator

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Summary
AccessionBT000510
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJens Stoye