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Nucleic Acids Res. 2014 Jan;42(Database issue):D910-6. doi: 10.1093/nar/gkt1052. Epub 2013 Nov 4.

dbPSHP: a database of recent positive selection across human populations.

Author information

1
Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China, Department of Anaesthesiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China, Department of Pathology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China, Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China, State Key Laboratory in Cognitive and Brain Sciences, The University of Hong Kong, Hong Kong SAR, China and Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.

Abstract

The dbPSHP database (http://jjwanglab.org/dbpshp) aims to help researchers to efficiently identify, validate and visualize putative positively selected loci in human evolution and further discover the mechanism governing these natural selections. Recent evolution of human populations at the genomic level reflects the adaptations to the living environments, including climate change and availability and stability of nutrients. Many genetic regions under positive selection have been identified, which assist us to understand how natural selection has shaped population differences. Here, we manually collect recent positive selections in different human populations, consisting of 15,472 loci from 132 publications. We further compiled a database that used 15 statistical terms of different evolutionary attributes for single nucleotide variant sites from the HapMap 3 and 1000 Genomes Project to identify putative regions under positive selection. These attributes include variant allele/genotype properties, variant heterozygosity, within population diversity, long-range haplotypes, pairwise population differentiation and evolutionary conservation. We also provide interactive pages for visualization and annotation of different selective signals. The database is freely available to the public and will be frequently updated.

PMID:
24194603
PMCID:
PMC3965004
DOI:
10.1093/nar/gkt1052
[Indexed for MEDLINE]
Free PMC Article

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