Accurate phylogenetic classification of variable-length DNA fragments.

TitleAccurate phylogenetic classification of variable-length DNA fragments.
Publication TypeJournal Article
Year of Publication2007
AuthorsMcHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I
JournalNature methods
Date Published2007 Jan
KeywordsAnimals, Archaea, Arthropods, Ascomycota, Bacteria, Chordata, DNA, Eukaryotic Cells, Genome, Genomics, Industrial Waste, Phylogeny, Sargassum, Software Validation

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 >or=1 kb with high specificity.

Alternate JournalNat. Methods