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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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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.
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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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Some researchers gain access to large amounts of data without interacting with a single research participant. Instead, they use existing records to answer various research questions. This type of research approach is known as archival research. Archival research relies on looking at past records or data sets to look for interesting patterns or relationships. For example, a researcher might access the academic records of all individuals who enrolled in college within the past ten years and...
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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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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.
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DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Archiving

Background:

  • The DNA Data Bank of Japan (DDBJ) Center is a key member of the International Nucleotide Sequence Database Collaboration (INSDC).
  • The DDBJ Center currently manages nucleotide sequence data and the Japanese Genotype-phenotype Archive (JGA) for human data.
  • Existing infrastructure supports large-scale genome sequence analysis via the NIG supercomputer.

Purpose of the Study:

  • To report on the database activities of INSDC and JGA over the past year.
  • To announce the establishment and services of the new Genomic Expression Archive (GEA).
  • To detail the development of submission, retrieval, and analysis services, including a secure platform for personal human genomes.

Main Methods:

  • Development and implementation of the DDBJ BioSample validator for automated data submission.
  • Leveraging the NIG supercomputer for large-scale genome sequence analysis.
  • Establishing a secure platform for handling personal human genomic data.

Main Results:

  • The Genomic Expression Archive (GEA) has been successfully launched at the DDBJ Center.
  • The DDBJ BioSample validator automates and corrects data submission formats, issuing necessary warnings.
  • Enhanced services for data submission, retrieval, and analysis are now available, including specialized handling of personal human genomes.

Conclusions:

  • The DDBJ Center has expanded its data archiving and analysis services with the launch of GEA.
  • Automated validation and a secure platform improve the efficiency and integrity of genomic data management.
  • These developments support the broader scientific community by providing robust resources for functional genomics research.