文章基本信息

标题：Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists
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作者：Wiley, Laura K. ; Sivley, R. Michael ; Bush, William S. 等
期刊名称：Database
印刷版ISSN：1758-0463
电子版ISSN：1758-0463
出版年度：2013
卷号：2013
DOI：10.1093/database/bat056
出版社：Oxford University Press
摘要：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