Koji Doi

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Additional file 2: of Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data

Table S1. Detection performance of SNP by artificially-modified rice genome. (XLSX 13 kb)

Additional file 1: of Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data

Figure S1. An example of bidirectional alignment. SNP was detected by the single-directional alig... more Figure S1. An example of bidirectional alignment. SNP was detected by the single-directional alignment. Insertion, deletion, inversion, and translocation were detected by the bidirectional alignment. The polymorphic edge, i.e., the mismatch detected first, is indicated with a vertical bar and location on the chromosome. Summarized data following # are the order of chromosome number and position of the edge detected by matching from the 5′-end, chromosome number and position from the 3′-end, direction, type of polymorphism, and size of insertion or deletion. The next line of the summarized data is the sequence of k-mers for detection of map location of 5′- and 3′- ends following the size of the margin described in 'Mapping by join command' section in Methods. (PPTX 30 kb)

Ontology Using Role Concept Recognized on Biological Relationships and Its Application

Genome Informatics, 2003

The biological ontology applied to all organisms is useful to exchange genome informatics and toc... more The biological ontology applied to all organisms is useful to exchange genome informatics and tocompare them. On one hand, biological domain ontology for speci c organism is necessary to providecontrolled common vocabularyforresearchersinterested inthe eld. Inthebiological domainontology,gene, gene product, and biological process should be reasonably connected for covering knowledge ofmolecular genetics and genome informatics. Role concept [1, 2] is suitable to represent a changeabilityof gene and gene product in cell. We designed a prototype of biological domain ontology using roleconcept and relationship.Rice Ontology (RO) has been developed as biological domain ontology. Rice is an important modelplant of genome research, and various data sets such as sequence information, full-length cDNA, andmicroarray, have been published. RO is expected to support the overview of these informatics dataand the inference of the pathway or the function.

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Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data

BMC Bioinformatics, 2019

Background: Accurate detection of polymorphisms with a next generation sequencer data is an impor... more Background: Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable. Result: We demonstrate two new detection methods of polymorphisms focusing on the Polymorphic Edge (PED). In the matching between two homologous sequences, the first mismatched base to appear is the SNP, or the edge of the structural variation. The first method is based on k-mers from short reads and detects polymorphic edges with k-mers for which there is no match between target and control, making it possible to detect SNPs by direct comparison of short-reads in two datasets (target and control) without a reference genome sequence. The second method is based on bidirectional alignment to detect polymorphic edges, not only SNPs but also insertions, deletions, inversions and translocations. Using these two methods, we succeed in making a high-quality comparison map between rice cultivars showing good match to the theoretical value of introgression, and in detecting specific large deletions across cultivars. Conclusions: Using Polymorphic Edge Detection (PED), the k-mer method is able to detect SNPs by direct comparison of short-reads in two datasets without genomic alignment step, and the bidirectional alignment method is able to detect SNPs and structural variations from even single-end short-reads. The PED is an efficient tool to obtain accurate data for both SNPs and structural variations.

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Generation challenge Programme (GCP) platform for crop research

The Generation Challenge Programme (GCP; www.generationcp.org) is a global crop research consorti... more The Generation Challenge Programme (GCP; www.generationcp.org) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: Shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform.

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PosMed: ranking genes and bioresources based on Semantic Web Association Study

Nucleic Acids Research, 2013

Positional MEDLINE (PosMed; ) is a powerful Semantic Web Association Study engine that ranks biom... more Positional MEDLINE (PosMed; ) is a powerful Semantic Web Association Study engine that ranks biomedical resources such as genes, metabolites, diseases and drugs, based on the statistical significance of associations between user-specified phenotypic keywords and resources connected directly or inferentially through a Semantic Web of biological databases such as MEDLINE, OMIM, pathways, co-expressions, molecular interactions and ontology terms. Since 2005, PosMed has long been used for in silico positional cloning studies to infer candidate disease-responsible genes existing within chromosomal intervals. PosMed is redesigned as a workbench to discover possible functional interpretations for numerous genetic variants found from exome sequencing of human disease samples. We also show that the association search engine enhances the value of mouse bioresources because most knockout mouse resources have no phenotypic annotation, but can be associated inferentially to phenotypes via genes and biomedical documents. For this purpose, we established text-mining rules to the biomedical documents by careful human curation work, and created a huge amount of correct linking between genes and documents. PosMed associates any phenotypic keyword to mouse resources with 20 public databases and four original data sets as of May 2013.

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The Vigna angularis complex: Genetic variation and relationships revealed by RAPD analysis, and their implications for in situ conservation and domestication

Genetic Resources and Crop Evolution - GENET RESOUR CROP EVOLUTION, 2000

The present study, using RAPD analysis, was undertaken to characterize genetic variation in three... more The present study, using RAPD analysis, was undertaken to characterize genetic variation in three forms of V. angularis, cultivated, wild and weedy forms, and their relationships. The materials used consisted of 171 individuals (plants) or cultivars from 23 populations including 5 wild populations, 6 weedy populations, 6 cultivated populations and 6 populations with plants having wild and weedy or intermediate morphology, denoted here as complex populations. The materials used were collected on Honshu Island, Japan and seeds collected directly from the field were germinated for DNA extraction. In addition, 6 landrace accessions of V. angularis from the genebank were also analyzed. Genetic variation was highest in the wild form (Hg= 0.132; GD = 0.388), followed by the weedy form (Hg= 0.124; GD = 0.341) and the least in the cultivated form (Hg= 0.079; GD = 0.274). Intra-population genetic variation was high in the weedy and in the wild populations. However, inter-population was greate...

Analysis of the Genetic Diversity in the Vigna minima Complex and Related Species in East Asia

Journal of Plant Research, 2000

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A pair of invertedly repeated genes in Chlamydomonas reinhardtii encodes a zygote-specific protein whose expression is UV-sensitive

Current Genetics, 1999

Uniparental inheritance of the chloroplast genome has been observed in a wide variety of green pl... more Uniparental inheritance of the chloroplast genome has been observed in a wide variety of green plants. In Chlamydomonas this phenomenon, which can be selectively inhibited by UV irradiation of mt(+) gametes, has been shown cytologically to be due to the preferential degradation of mt(-)-derived chloroplast nucleoids in young zygotes. The zygote-specific pair of zys1 genes, zys1A and zys1B, is expressed earliest among five genes isolated from a &quot;10-min&quot; zygote library. We report here that the ZYS1 protein, which is encoded by the invertedly duplicated zys1 gene, accumulates in zygotes and is localized in nuclei. In addition, when mt(+) gametes (but not mt(-) gametes) are UV-irradiated before mating, only very limited accumulation of ZYS1 protein can be detected in the resulting zygotes.

AFLP analysis of diploid species in the genus Vigna subgenus Ceratotropis

Genetic Resources and Crop Evolution, 2002

A representative set of germplasm of genusVigna subgenus Ceratotropis specieswas used to analyze ... more A representative set of germplasm of genusVigna subgenus Ceratotropis specieswas used to analyze genetic diversity using amplified fragment lengthpolymorphism (AFLP) methodology. The germplasm was selected based onmorphological diversity and geographic origin and includes 18 out of the 21species in the subgenus Ceratotropis. Genetic diversitywithin and between taxa was measured using information generated by AFLP bandpolymorphism from which Jaccard's similarity coefficient

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