P0329DBCLS SRA: Integrated Search of Public NGS Database, the Sequence Read Archive (SRA), and Its Relevant Databases
DBCLS SRA: Integrated Search of Public NGS Database, the Sequence Read Archive (SRA), and Its Relevant Databases
High-throughput sequencing, also called next-generation sequencing (NGS), is widely used for omics analysis with non-classical model organisms, and its numerous sequence read data have been archived in public database, the sequence read archive (SRA) with their experimental information as metadata by DDBJ, EBI and NCBI. As of October 2016, 8.6 peta bp of reads are archived in about 86,000 projects.
We categorized SRA data by study types (e. g. whole genome study, transcriptomics, and metagenomics), sequencing platforms, and species or cell lines of samples. To visualize these information, we developed a web-service called DBCLS SRA (http://sra.dbcls.jp/).
Recently, project information archived in SRA has moved to BioProject database, and sample information has also moved to BioSample databases. In addition, transcriptome data with NGS have archived in not only SRA but also GEO as gene expression databases. We therefore connected corresponding submissions in various databases.
For plant and animal researchers, DBCLS SRA provides the NGS data list of sample species or strains under same taxonomy level such as species, genus, families in one search. For example, they can retrieve Oryza sativa indica or japonica strain data by searching Oryza sativa. Users also list up other Oryza species data as a parent taxonomy.