Accurate phylogenetic classification of variable-length DNA fragments

McHardy, Alice Carolyn, Martin, Hector Garcia, Tsirigos, Aristotelis, Hugenholtz, Philip and Rigoutsos, Isidore (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods, 4 1: 63-72. doi:10.1038/NMETH976


Author McHardy, Alice Carolyn
Martin, Hector Garcia
Tsirigos, Aristotelis
Hugenholtz, Philip
Rigoutsos, Isidore
Title Accurate phylogenetic classification of variable-length DNA fragments
Journal name Nature Methods   Check publisher's open access policy
ISSN 1548-7091
1548-7105
Publication date 2007-01
Sub-type Article (original research)
DOI 10.1038/NMETH976
Volume 4
Issue 1
Start page 63
End page 72
Total pages 10
Place of publication London, England, U.K.
Publisher Nature Publishing Group
Language eng
Formatted abstract Metagenome studies have retrieved vast amounts of sequence data from a variety of environments leading to new discoveries and insights into the uncultured microbial world. Except for very simple communities, the encountered diversity has made fragment assembly and the subsequent analysis a challenging problem. A taxonomic characterization of metagenomic fragments is required for a deeper understanding of shotgun-sequenced microbial communities, but success has mostly been limited to sequences containing phylogenetic marker genes. Here we present PhyloPythia, a composition-based classifier that combines higher-level generic clades from a set of 340 completed genomes with sample-derived population models. Extensive analyses on synthetic and real metagenome data sets showed that PhyloPythia allows the accurate classification of most sequence fragments across all considered taxonomic ranks, even for unknown organisms. The method requires no more than 100 kb of training sequence for the creation of accurate models of sample-specific populations and can assign fragments ≥ 1 kb with high specificity.
Keyword Bacteria
Codon usage
Gene-transfer
Sequences
Reconstruction
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: ERA 2012 Admin Only
School of Chemistry and Molecular Biosciences
 
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