What's in the mix: phylogenetic classification of metagenome sequence samples.
Metagenomics is a novel field which deals with the sequencing and study of microbial organisms or viruses isolated directly from a particular environment. This has already provided a wealth of information and new insights for the inhabitants of various environmental niches. For a given sample, one would like to determine the phylogenetic provenance of the obtained fragments, the relative abundance of its different members, their metabolic capabilities, and the functional properties of the community as a whole. To this end, computational analyses are becoming increasingly indispensable tools. In this review, we focus on the problem of determining the phylogenetic identity of the sample fragments, a procedure known as 'binning'. This step is essential for the reconstruction of the metabolic capabilities of individual organisms or phylogenetic clades of a community, and the study of their interactions.
McHardy
Alice C
AC
Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA. mchardy@mpi-inf.mpg.de
Rigoutsos
Isidore
I
D000818:Animals; D001105:Archaea / Q000737:chemistry / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D001483:Base Sequence; D044822:Biodiversity; D018441:Biofilms / Q000145:classification; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000145:classification; D004783:Environmental Microbiology; D023281:Genomics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
D004247:DNA