Hervas Sergi, Sanz Esteve, Casillas Sònia, Pool John E, Barbadilla Antonio
Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain.
Servei de Genòmica i Bioinformàtica, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain.
Bioinformatics. 2017 Sep 1;33(17):2779-2780. doi: 10.1093/bioinformatics/btx301.
The recent compilation of over 1100 worldwide wild-derived Drosophila melanogaster genome sequences reassembled using a standardized pipeline provides a unique resource for population genomic studies (Drosophila Genome Nexus, DGN). A visual display of the estimated metrics describing genome-wide variation and selection patterns would allow gaining a global view and understanding of the evolutionary forces shaping genome variation.
Here, we present PopFly, a population genomics-oriented genome browser, based on JBrowse software, that contains a complete inventory of population genomic parameters estimated from DGN data. This browser is designed for the automatic analysis and display of genetic variation data within and between populations along the D. melanogaster genome. PopFly allows the visualization and retrieval of functional annotations, estimates of nucleotide diversity metrics, linkage disequilibrium statistics, recombination rates, a battery of neutrality tests, and population differentiation parameters at different window sizes through the euchromatic chromosomes. PopFly is open and freely available at site http://popfly.uab.cat .
最近使用标准化流程重新组装了1100多个全球野生果蝇黑腹果蝇基因组序列,这为群体基因组研究提供了独特资源(果蝇基因组数据库,DGN)。对描述全基因组变异和选择模式的估计指标进行可视化展示,将有助于全面了解塑造基因组变异的进化力量。
在此,我们展示了PopFly,这是一个基于JBrowse软件的面向群体基因组学的基因组浏览器,它包含了根据DGN数据估计的群体基因组参数的完整清单。该浏览器旨在自动分析和展示黑腹果蝇基因组内群体间和群体内的遗传变异数据。PopFly允许通过常染色体以不同窗口大小可视化和检索功能注释、核苷酸多样性指标估计、连锁不平衡统计、重组率、一系列中性检验以及群体分化参数。PopFly可在网站http://popfly.uab.cat上免费获取且开放使用。