title: Ensembl variation resources.
abstract: BACKGROUND
  The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics.
  
  
  METHODS
  The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl.
  
  
  CONCLUSIONS
  Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.forename: Fiona
authors.initials: F
authors.lastname: Cunningham
authors.forename: Daniel
authors.initials: D
authors.lastname: Rios
authors.forename: William M
authors.initials: WM
authors.lastname: McLaren
authors.forename: James
authors.initials: J
authors.lastname: Smith
authors.forename: Bethan
authors.initials: B
authors.lastname: Pritchard
authors.forename: Giulietta M
authors.initials: GM
authors.lastname: Spudich
authors.forename: Simon
authors.initials: S
authors.lastname: Brent
authors.forename: Eugene
authors.initials: E
authors.lastname: Kulesha
authors.forename: Pablo
authors.initials: P
authors.lastname: Marin-Garcia
authors.forename: Damian
authors.initials: D
authors.lastname: Smedley
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002417:Cattle; D030541:Databases, Genetic; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D020407:Internet; D015810:Linkage Disequilibrium; D051379:Mice; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D051381:Rats; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface
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