Journal Article

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists

Laura K. Wiley, R. Michael Sivley and William S. Bush

in Database

Volume 2013, issue ISSN: 0000-0000
Published online July 2013 | e-ISSN: 1758-0463 | DOI: http://dx.doi.org/10.1093/database/bat056

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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

Journal Article.  2004 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Ecology and Conservation ; Evolutionary Biology

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