Application of database on frequencies of nucleotide n-gram profiles to genomic analyses.

2017 Fiscal Year Final Research Report

• Project/Area Number: 15K14423
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Genome biology
• Research Institution: Nihon University
• Principal Investigator: KUWATA Fumiyuki 日本大学, 歯学部, 特任教授 (60120440)
• Co-Investigator(Kenkyū-buntansha): 谷口 奈央 福岡歯科大学, 口腔歯学部, 准教授 (60372885) ; 中野 善夫 日本大学, 歯学部, 教授 (80253459)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Keywords: 菌叢解析 / サポートベクターマシン

Outline of Final Research Achievements

In this study, we demonstrates construction of phylogenetic trees based on genome-wide comparisons based on n-gram profiles. n-gram frequency analysis was used to separate species that are difficult to distinguish based on 16S rRNA gene sequences. Next, the relative abundances of artificial bacterial species mixture were estimated. Frequencies of five continuous nucleotides were calculated from the obtained sequences and their proportional compositions were estimated by the combinations of frequencies from genomic data and samples. Origins of the fragments were determined by BLAST and were compared with the abundances based on nucleotide frequencies. The both results were agreed closely and furthermore the similar result obtained from 10 sequences of five continuous nucleotides with high entropy values. In addition, horisontal-transfered genes were estimated by one-class support vector machine based on continuous nucleotide frequencies within each genome.

Free Research Field

口腔生化学