DDBJ

DDBJ archives nucleotide sequence data and associated metadata to support storage, international exchange, and computational analysis of raw reads, assemblies, and functional annotations within the INSDC collaboration.

Key Features:

• Nucleotide Sequence Archive: DDBJ stores nucleotide sequences including raw sequence reads, assembly information, and functional annotations.
• Omics Archive (DOR): The DDBJ Omics Archive (DOR) stores quantitative genomics datasets derived from microarray analyses and high-throughput sequencing.
• Sequence Read Archive (DRA): The DRA archives raw sequencing reads generated by next-generation sequencing platforms for large-scale genomic analyses.
• Read Annotation Pipeline: A cloud computing-based, semi-automatic analytical system performing reference genome mapping, de novo assembly, and high-level structural and functional annotations of sequencing reads.
• BioProject Resource: BioProject provides structured metadata linking research projects to associated datasets across DDBJ databases.
• INSDC Collaboration: DDBJ exchanges sequence data with International Nucleotide Sequence Database Collaboration partners, including EBI and NCBI.

Scientific Applications:

• Genome sequencing: Storage and access to raw reads and assemblies to support genome assembly and annotation projects.
• Gene expression analysis: Archival of microarray and high-throughput sequencing expression datasets for transcriptome and differential expression studies.
• Functional genomics: Integration of sequence data and high-level annotations to support identification of gene function and regulatory elements.
• Comparative genomics: Provision of sequence and annotation data enabling cross-species and population-level genomic comparisons.

Methodology:

Semi-automatic read annotation using a cloud computing-based pipeline that performs reference genome mapping, de novo assembly, and high-level structural and functional annotations.