Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.
Database (Oxford)
; 2013: bat056, 2013.
Article
em En
| MEDLINE
| ID: mdl-23894185
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.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Sistemas de Gerenciamento de Base de Dados
/
Armazenamento e Recuperação da Informação
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Genômica
Idioma:
En
Ano de publicação:
2013
Tipo de documento:
Article