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wFleaBase: the Daphnia genome database.

John K Colbourne1, Vasanth R Singan, Don G Gilbert

  • 1Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA. jcolbour@cgb.indiana.edu

BMC Bioinformatics
|March 9, 2005
PubMed
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wFleaBase is a new genome database for Daphnia, a crucial freshwater organism. It provides tools for genetic and genomic data, supporting ecological and evolutionary research on this important model organism.

Area of Science:

  • Genomics
  • Bioinformatics
  • Ecology

Background:

  • Daphnia (water-flea) is a vital model organism in freshwater ecosystems with a long history of biological study.
  • The Daphnia Genomics Consortium (DGC) initiated a program to develop resources for studying genes related to ecological and evolutionary success.

Purpose of the Study:

  • To introduce wFleaBase, a novel genome database for the microcrustacean Daphnia.
  • To provide infrastructure for curating, archiving, and sharing genetic, molecular, and functional genomic data for Daphnia.

Main Methods:

  • wFleaBase is built using core components from the Generic Model Organism Database (GMOD) project.
  • The database incorporates bioinformatics tools for data retrieval and analysis.

Main Results:

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  • wFleaBase currently supports searching and extracting information from expressed sequence tags, genome survey sequences, and full genome sequencing projects.
  • Future integration includes preliminary genetic maps and the nearly complete Daphnia pulex genome sequence with gene predictions and ortholog assignments.

Conclusions:

  • wFleaBase serves as a valuable resource for the ecological and evolutionary research community studying Daphnia.
  • The database aims to expand content and integrate genetic and functional genomics with population-level environmental responses.