title: Accurate phylogenetic classification of variable-length DNA fragments.
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 >or=1 kb with high specificity.
authors.affiliation: Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA.
authors.forename: Alice Carolyn
authors.initials: AC
authors.lastname: McHardy
authors.forename: Héctor García
authors.initials: HG
authors.lastname: Martín
authors.forename: Aristotelis
authors.initials: A
authors.lastname: Tsirigos
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics; D001181:Arthropods / Q000235:genetics; D001203:Ascomycota / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D043344:Chordata / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000145:classification* / Q000235:genetics*; D005057:Eukaryotic Cells; D016678:Genome; D023281:Genomics / Q000379:methods*; D007220:Industrial Waste; D010802:Phylogeny; D044647:Sargassum / Q000382:microbiology; D012986:Software Validation
chemical_list: D007220:Industrial Waste; D004247:DNA