Bioinformatics Lab. English のバックアップ(No.1)

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Welcome to Bioinformatics Laboratory, Information Engineering, Niigata University.

Research Fields of Interest

It is one of the most important tasks of life science to unveil unknown basic knowledge from a large amount of accumulated information of genomic sequences. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional complex data on a two-dimensional map. We developed a modified SOM (Batch Learning SOM; BLSOM) for comprehensive analyses of species-specific genomic sequence characteristics.

1. Comparative genome analyses for unveiling genome signature

We found that BLSOM could classify genomic sequence fragments according to species without any information other than oligonucleotide frequencies in a wide range of genomes. The BLSOM, which can systematically characterize species-specific genome signature of all prokaryotes and eukaryotes analyzable, proves a new powerful bioinformatics strategy to study biodiversity and molecular evolution.

2. A novel bioinformatics strategy for unveiling microbial diversity and protein functions of metagenome sequences

Metagenomic approach, which is the genome analysis on a mixture of uncultured microorganisms, has been recently developed to search for novel and industrially useful genes and to study microbial diversity in a wide variety of environments. Using a BLSOM, most of the sequences obtained by metagenomic studies were classified (self-organized) according to phylotypes without any phylogenetic information. Because the BLSOM is a powerful tool for phylogenetic classification of genomic fragments, BLSOM could provide a new systematic strategy for revealing basic knowledge obtained from uncultured microorganisms including viruses in a wide variety of environmental samples.