PopHuman: the human population genomics browser

被引：27

作者：

Casillas, Sonia ^{[1
,2
]}

Mulet, Roger ^{[1
,2
]}

Villegas-Miron, Pablo ^{[3
]}

Hervas, Sergi ^{[1
,2
]}

Sanz, Esteve ^{[4
]}

Velasco, Daniel ^{[1
,2
]}

Bertranpetit, Jaume ^{[3
]}

Laayouni, Hafid ^{[3
,5
]}

Barbadilla, Antonio ^{[1
,2
,4
]}

机构：

[1] Univ Autonoma Barcelona, Inst Biotecnol & Biomed, E-08193 Barcelona, Spain

[2] Univ Autonoma Barcelona, Dept Genet & Microbiol, E-08193 Barcelona, Spain

[3] Univ Pompeu Fabra, Inst Evolutionary Biol UPF CSIC, Doctor Aiguader 88 PRBB, Barcelona 08003, Catalonia, Spain

[4] Univ Autonoma Barcelona, Serv Genom & Bioinformat, E-08193 Barcelona, Spain

[5] ESCI UPF, Bioinformat Studies, Pg Pujades 1, Barcelona 08003, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2018年 / 46卷 / D1期

关键词：

ADAPTIVE PROTEIN EVOLUTION; RECENT POSITIVE SELECTION; NATURAL-SELECTION; STATISTICAL TESTS; GENETIC-VARIATION; RAPID EVOLUTION; HAPLOTYPE MAP; DNA; SEQUENCE; RECOMBINATION;

D O I：

10.1093/nar/gkx943

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The 1000 Genomes Project (1000GP) represents the most comprehensiveworld-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat.

引用

页码：D1003 / D1010

页数：8

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