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Related Experiment Videos

DDBJ with new system and face.

H Sugawara1, O Ogasawara, K Okubo

  • 1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan.

Nucleic Acids Research
|October 27, 2007
PubMed
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The DNA Data Bank of Japan (DDBJ) released over 1.88 million nucleotide sequences, including cricket cDNAs and medaka genomes. New data retrieval tools enhance sequence and annotation searching capabilities.

Area of Science:

  • Genomics
  • Bioinformatics
  • Nucleotide Sequence Databases

Background:

  • The DNA Data Bank of Japan (DDBJ) is a critical repository for nucleotide sequence data.
  • Continuous updates and system improvements are essential for maintaining a high-quality biological database.

Purpose of the Study:

  • To report on the data collection and release activities of DDBJ from July 2006 to June 2007.
  • To introduce new system upgrades and data retrieval tools implemented at DDBJ.
  • To highlight the inclusion of significant datasets such as high-throughput cricket cDNAs and medaka draft genomes.

Main Methods:

  • Data collection and curation of nucleotide sequences.
  • System upgrades to enhance computational infrastructure.
  • Development and implementation of the All-round Retrieval for Sequence and Annotation (ARSA) tool.

Related Experiment Videos

  • Integration with the International Nucleotide Sequence Database Collaboration (INSDC) for keyword searching in Feature/Qualifier fields.

    • Main Results:

    • DDBJ released 1,880,115 entries, totaling 1,134,086,245 bases.
    • Included high-throughput cDNA data from crickets and high-quality draft genome data from medaka.
    • A new, efficient data retrieval tool, ARSA, was launched, enabling keyword searches within INSDC Feature/Qualifier data.
    • Computer systems were upgraded in March 2007.

    Conclusions:

    • DDBJ has significantly expanded its nucleotide sequence database with diverse and high-quality data.
    • The introduction of ARSA enhances data accessibility and searchability for researchers.
    • Ongoing system and website improvements demonstrate DDBJ's commitment to providing advanced bioinformatics resources.