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

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 ha...

Full description

Saved in:
Bibliographic Details
Published in:Database : the journal of biological databases and curation 2013, Vol.2013, p.bat056-bat056
Main Authors: Wiley, Laura K, Sivley, R Michael, Bush, William S
Format: Article
Language:English
Subjects:
Algorithms
Database Management Systems
Databases, Genetic
Genomics
Information Storage and Retrieval
Original
Search Engine
Citations: Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1758-0463
1758-0463
DOI:10.1093/database/bat056