A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)

Microorganisms

Yuki Iwasaki¹  Takashi Abe¹  Kennosuke Wada¹  Yoshiko Wada¹ 

[1] Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:

关键词: metagenome;    oligonucleotide composition;    influenza virus;    big data;    peptide composition;    bioinformatics;    SOM;    genome signature;    microbial community;   

DOI  :  10.3390/microorganisms1010137

来源: mdpi

【 摘 要 】

With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.

【 授权许可】

CC BY   
© 2013 by the authors; licensee MDPI, Basel, Switzerland.