Genomics | Bioinformatics | Evolutionary/Comparative Genetics
The Drosophila genome variation browser
Miquel Ràmia*, Pablo Librado, Sònia Casillas, Julio Rozas, Antonio Barbadilla
*Corresponding author: Miquel Ràmia
Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
F1000Posters 2010, 1: 281 (poster) [ENGLISH]
Poster [7.45 MB]
Society for Molecular Biology and Evolution 2010 meeting, 4 - 8 Jul 2010, P-S20-42
Population genetics studies have so far been based on fragmentary and non-random samples of the genome, providing a partial and often biased view of the population processes. The complete sequencing of 192 individuals from a single population of Drosophila melanogaster will allow getting a global view of genomic variation and an understanding of the evolutionary forces shaping the patterns of polymorphism and divergence along the genome. We present a novel genome browser, the “Drosophila Genome Variation Browser” (DGVBrowser), for the automatic estimation and representation of genetic variation using Gbrowse, PDA, MKT and VariScan.
The input data are aligned haplotype intraspecific DNA sequences, which might also ideally comprise an outgroup. The output results include nucleotide and indel variation frequencies, summary measures of nucleotide diversity, linkage disequilibrium, and several neutrality tests. The DGVBrowser also allows performing custom analyses on-the-fly using user-selected parameters. Remarkably, this genome browser tool can be easily customized to any other species for which DNA polymorphism data is available at the genome scale.
The DGVBrowser is thus a timely tool for the present golden age of the study of genome variation. This browser is free and open to all users.
No relevant conflicts of interest declared.
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