A database and API for variation, dense genotyping and resequencing data

被引：28

作者：

Rios, Daniel ^{[1
]}

McLaren, William M. ^{[1
]}

Chen, Yuan ^{[1
]}

Birney, Ewan ^{[1
]}

Stabenau, Arne ^{[1
]}

Flicek, Paul ^{[1
]}

Cunningham, Fiona ^{[1
]}

机构：

[1] European Bioinformat Inst, Cambridge CB10 1SD, England

来源：

BMC BIOINFORMATICS | 2010年 / 11卷

基金：

英国医学研究理事会; 英国惠康基金;

关键词：

SEQUENCE VARIATION; ENSEMBL; RESOURCES; PROJECT; MAP;

D O I：

10.1186/1471-2105-11-238

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources. Results: Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes. These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation. The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl project in a number of database and application environments. Conclusions: Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at http://www.ensembl.org.

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