SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access

Background: In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. Results: We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Jorge Amigo, Antonio Salas, Christopher Phillips, Ángel Carracedo
• Keywords: BMCBI 2008, Data Mart, Databases, Population Information