Positive selection databases | Population genetic data analysis
Natural selection plays a crucial role in the evolution of species, where random mutations are undergoing positive, purifying or balancing selection for adaptation to the living environments including climate change, availability and stability of nutrients, introduction of novel disease agents, dispersed niche, etc.
The database contained curated publications about positive selection in different human populations, which consisted of over 15,000 loci from either publications attempting to study positively selected genomic locus and gene related to specific functions/traits/diseases, or publications to detect the genome-wide selective signals with different statistical methods.
Contains signatures of recent natural selection in modern humans. 1000 Genomes Selection Browser offers a genome-wide browser to communicate the results from three different populations of West African, Northern European and East Asian ancestry. The genome browser gives a visual impression of the genetic variation in a genomic region of interest and offers functionality for an array of down-stream analyses. The database offers a large number of test statistics and a fine-grained resequencing data.
Contains ortholog groups for most completely sequenced and annotated eukaryotes for a number of completely sequenced and annotated prokaryotes. OrthoMCL-DB provides a wealth of functionality, including domain architecture for each group, phyletic patterns for each group and advanced querying, including phylogenetic pattern searches. The database gives also access to OrthoMCL, which groups proteins into “ortholog groups” (i.e. set of proteins across one or more species that represent putative orthologs and in-paralogs).
Offers access to results of systematic branch-site tests for positive selection on all internal branches of selected clades. Selectome is a database of positive selection that allows detection of episodic selection. This online resource provides users with access to precomputed estimates of positive selection from the branch-site test mapped to branches of gene trees, and to amino-acid sites of multiple sequence alignments (MSAs).
Provides a repository for an experiment comprising rainfall-manipulation practiced on Arabidopsis thaliana. dryAR compiles a high-throughput field experiment which has generated an important dataset to study natural selection and adaptation in the context of global climate change at the genetic level.
Gathers information related to adaptation events along the human evolutionary history. PopHumanScan is a repository supplying graphical representation of each signature of selection within the empirical distributions of the corresponding DNA diversity statistic across populations. Besides, it includes structural and functional annotations of the region, links to external databases and cross-references to more than 200 publications.
An integrative and hierarchical database focusing on positive selection of human genome. [email protected] is a valuable and useful resource for finding and verifying signals of natural selection. It provides two user interfaces, data query and data visualization.