DNA Polymorphism Database from New-Generation Sequence Read Archive and Analytical Workflow

With the development in New-Generation Sequencing (NGS), many DNA polymorphism datasets of various species and strains have been released as open data on the internet. These resources are not designed to effectively explore the knowledge associated with breeding science in parallel. Individual DNA polymorphism datasets indicate different precisions because their experimental conditions differ among studies. To integrate multiple DNA polymorphism datasets, uniform experimental conditions are required. In this research, we constructed an integrated database and analytical workflows called “DNA Polymorphism Annotation Database (DNApod)” (http://tga.nig.ac.jp/dnapod/). The DNApod database supports DNA polymorphisms and their annotations with known gene structures, which were analyzed by uniform experimental conditions from data in the NGS archive database. Our scope is to provide datasets ranging from bacteria to plants and animals. The DNApod database currently covers only plant lines, which contain data derived from 679 rice lines, 404 maize lines, and 66 sorghum lines. For utilizing the knowledge of model organisms to other organisms, we provide an application of amino acid sequence alignment between orthologous regions of DNApod data. Then, a DNApod workflow was constructed where users can analyze their original NGS data using same experimental conditions with the DNApod database. The DNApod workflow was integrated as a workflow of “DDBJ Read Annotation Pipeline (DDBJ pipeline)” (http://p.ddbj.nig.ac.jp/).

In this presentation, we will introduce highlighted functions of the DNApod database and the analytical workflow.