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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genomic Imprinting and Inheritance02:30

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Genome Size and the Evolution of New Genes03:21

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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Genomic DNA in Prokaryotes00:46

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
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Updated: Jan 31, 2026

A Semantic Priming Event-related Potential ERP Task to Study Lexico-semantic and Visuo-semantic Processing in Autism Spectrum Disorder
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TogoGenome/TogoStanza: modularized Semantic Web genome database.

Toshiaki Katayama1, Shuichi Kawashima1, Shinobu Okamoto1

  • 1Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa-shi, Chiba, Japan.

Database : the Journal of Biological Databases and Curation
|January 10, 2019
PubMed
Summary
This summary is machine-generated.

TogoGenome utilizes Semantic Web technology for integrated genomic data and flexible searches. This genome database offers advanced comparative genomics and a reusable modular framework, TogoStanza.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Semantic Web technologies

Background:

  • Genomic data integration is challenging due to heterogeneity.
  • Existing databases often lack flexibility and advanced search capabilities.
  • Semantic Web technologies offer a solution for data integration and querying.

Purpose of the Study:

  • To introduce TogoGenome, a genome database built on Semantic Web technology.
  • To enable flexible semantic searches and data integration.
  • To provide a framework for semantic comparative genomics and reusable database modules.

Main Methods:

  • Utilized Resource Description Framework (RDF) for data storage.
  • Employed SPARQL Protocol and RDF Query Language (SPARQL) for dynamic web page generation and querying.
  • Developed a semantic-faceted search system based on ontologies.
  • Implemented a modular structure using TogoStanza for reusable information blocks.

Main Results:

  • TogoGenome successfully integrates heterogeneous genomic data.
  • The database supports flexible semantic searches across functional annotations, taxonomy, phenotypes, and environments.
  • Semantic comparative genomics is enabled, allowing observation of pan-organism or organism-specific genes.
  • TogoStanza provides a reusable framework for constructing database modules.

Conclusions:

  • TogoGenome offers a powerful, flexible, and integrated approach to genomic data management and analysis.
  • The modular TogoStanza framework enhances reusability and database construction.
  • The database and framework are freely available, promoting open science and further development.