title: Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.
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. Database URL: https://github.com/bushlab/mynclist.
authors.affiliation: Department of Biomedical Informatics, Center for Human Genetics Research, Vanderbilt University, 2215 Garland Ave, Nashville, TN 37232, USA.
authors.forename: Laura K
authors.initials: LK
authors.lastname: Wiley
authors.forename: R Michael
authors.initials: RM
authors.lastname: Sivley
authors.forename: William S
authors.initials: WS
authors.lastname: Bush
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D030541:Databases, Genetic; D023281:Genomics; D016247:Information Storage and Retrieval; D057386:Search Engine
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