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- Title
Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.
- Authors
Wiley, Laura K.; Sivley, R. Michael; Bush, William S.
- Abstract
Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks.
- Subjects
RELATIONAL databases; GENETICS; INFORMATION retrieval; GENOMICS; ANNOTATIONS
- Publication
Database: The Journal of Biological Databases & Curation, 2013, Vol 2013, p1
- ISSN
1758-0463
- Publication type
Article
- DOI
10.1093/database/bat056