PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup.
Drosophila pseudoobscura is a classic model system for the study of evolutionary genetics and genomics. Given this long-standing interest, many genome sequences have accumulated for D. pseudoobscura and closely related species D. persimilis, D. miranda, and D. lowei. To facilitate the exploration of genetic variation within species and comparative genomics across species, we present PseudoBase, a database that couples extensive publicly available genomic data with simple visualization and query tools via an intuitive graphical interface, amenable for use in both research and educational settings. All genetic variation (SNPs and indels) within the database is derived from the same workflow, so variants are easily comparable across data sets. Features include an embedded JBrowse interface, ability to pull out alignments of individual genes/regions, and batch access for gene lists. Here, we introduce PseudoBase, and we demonstrate how this resource facilitates use of extensive genomic data from flies of the Drosophila pseudoobscura subgroup.
Duke Scholars
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Related Subject Headings
- Species Specificity
- Genomics
- Genome
- Drosophila
- Developmental Biology
- Databases, Genetic
- Animals
- 3105 Genetics
- 0604 Genetics
- 0603 Evolutionary Biology
Citation
Published In
DOI
EISSN
ISSN
Publication Date
Volume
Issue
Start / End Page
Related Subject Headings
- Species Specificity
- Genomics
- Genome
- Drosophila
- Developmental Biology
- Databases, Genetic
- Animals
- 3105 Genetics
- 0604 Genetics
- 0603 Evolutionary Biology