PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup.

Accepted

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Korunes, KL; Myers, RB; Hardy, R; Noor, MAF

Published Date

  • December 2021

Published In

Volume / Issue

  • 15 / 1

Start / End Page

  • 38 - 44

PubMed ID

  • 33319644

Pubmed Central ID

  • 33319644

Electronic International Standard Serial Number (EISSN)

  • 1933-6942

International Standard Serial Number (ISSN)

  • 1933-6934

Digital Object Identifier (DOI)

  • 10.1080/19336934.2020.1864201

Language

  • eng