A bioinformatics strategy for revealing microbial community structures and metabolic pathways by reconstructing multiple genomes from metagenomic sequences.

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Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes useful in medical and industrial applications. BLSOM is the most suitable for phylogenetic assignment of metagenomic sequences because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition.We constructed oligonucleotide-BLSOMs for all available sequences from species-known genomes, and by mapping metagenomic sequences on this large-scale BLSOMs, we could predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms including viruses. This software will be freely available at our website. We also developed another BLSOM strategy for clustering metagenomic sequences according to genome, and for function prediction of poorly-characterized protein genes obtained from metagenome analysis.