Aki Hirai

Sequence-specific error profile of Illumina sequencers

We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers.

System Biology Approach for Elucidating the Relationship Between Indonesian Herbal Plants and the Efficacy of Jamu

Jamu is Indonesian herbal medicine made from a mixture of several plants. Some plants perform as main ingredients and the others as supporting ingredients. By utilizing biplot configuration, we explored the relationship between Indonesian herbal plants and the efficacy of jamu. Among 465 plants used in 3138 jamu, we determined that 190 plants were efficacious in at least one efficacy. We therefore consider these plants to be the main ingredients of jamu. The other 275 plants are considered to be supporting ingredients in jamu because their efficacy has not been established.

Ontology Checking and Integration of Crude-Drug and Kampo Information

Motivation: Wiki-based databases are becoming popular in biology research, but many of them do not provide a measure to control vocabulary (ontology) of input data despite their use in multi-user environment. We present an extension to MediaWiki, the most popular wiki-based platform, which realizes implementation of word checks and data integration at the user-level. With this functionality, any user can create integrated databases with controlled vocabularies inside wiki. Results: Over 150 crude-drug information and 300 Kampo formulas were integrated with >1500 plant genus information. All data are accessible at http://metabolomics.jp/wiki/. Availability: PHP source codes are available at http://metabolomics.jp/wiki/Metabolomics.JP:About. Introduced wiki commands are summarized at http://metabolomics.jp/wiki/Doc:Extensions. Keywords-wiki; database; Kampo formula; crude drug

Multivariate Analysis of Analytical Chemistry Data and Utility of the KNApSAcK Family Database to Understand Metabolic Diversity in Medicinal Plants

Due to the advances in computational sciences and analytical chemistry, metabolome analysis, which aims to elucidate metabolic diversity in organisms, has been demonstrated. The metabolomic approach has been frequently employed in medicinal plant studies because it can comprehensively and simultaneously analyze numerous metabolites with medicinal properties. To demonstrate metabolome analysis of medicinal plants, this chapter introduces: (1) comprehensive metabolite analysis based on analytical chemistry, (2) multivariate analysis of analytical chemistry data, and (3) a metabolite database search to identify signal processing in chemical analysis. In particular, the utility and role of the KNApSAcK Family database, which is a medicinal plant database connected with metabolites constructed by our group, are explained in detail. Additionally, this chapter describes the effectiveness and potential of computational systems biology in medicinal plant research.