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

Publication ,  Journal Article
Korunes, KL; Myers, RB; Hardy, R; Noor, MAF
Published in: Fly
December 2021

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.

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Published In

Fly

DOI

EISSN

1933-6942

ISSN

1933-6934

Publication Date

December 2021

Volume

15

Issue

1

Start / End Page

38 / 44

Related Subject Headings

  • Species Specificity
  • Genomics
  • Genome
  • Drosophila
  • Developmental Biology
  • Databases, Genetic
  • Animals
  • 3105 Genetics
  • 0604 Genetics
  • 0603 Evolutionary Biology
 

Citation

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Korunes, K. L., Myers, R. B., Hardy, R., & Noor, M. A. F. (2021). PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup. Fly, 15(1), 38–44. https://doi.org/10.1080/19336934.2020.1864201
Korunes, Katharine L., Russell B. Myers, Ryan Hardy, and Mohamed A. F. Noor. “PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup.Fly 15, no. 1 (December 2021): 38–44. https://doi.org/10.1080/19336934.2020.1864201.
Korunes KL, Myers RB, Hardy R, Noor MAF. PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup. Fly. 2021 Dec;15(1):38–44.
Korunes, Katharine L., et al. “PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup.Fly, vol. 15, no. 1, Dec. 2021, pp. 38–44. Epmc, doi:10.1080/19336934.2020.1864201.
Korunes KL, Myers RB, Hardy R, Noor MAF. PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup. Fly. 2021 Dec;15(1):38–44.

Published In

Fly

DOI

EISSN

1933-6942

ISSN

1933-6934

Publication Date

December 2021

Volume

15

Issue

1

Start / End Page

38 / 44

Related Subject Headings

  • Species Specificity
  • Genomics
  • Genome
  • Drosophila
  • Developmental Biology
  • Databases, Genetic
  • Animals
  • 3105 Genetics
  • 0604 Genetics
  • 0603 Evolutionary Biology