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Open Access Database

wFleaBase: the Daphnia genome database

John K Colbourne1*, Vasanth R Singan2 and Don G Gilbert3

Author Affiliations

1 Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana USA

2 School of Informatics, Indiana University, Bloomington, Indiana USA

3 Department of Biology, Indiana University, Bloomington, Indiana USA

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BMC Bioinformatics 2005, 6:45  doi:10.1186/1471-2105-6-45

Published: 7 March 2005

Abstract

Background

wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Commonly known as the water-flea, Daphnia's ecological merit is unequaled among metazoans, largely because of its sentinel role within freshwater ecosystems and over 200 years of biological investigations. By consequence, the Daphnia Genomics Consortium (DGC) has launched an interdisciplinary research program to create the resources needed to study genes that affect ecological and evolutionary success in natural environments.

Discussion

These tools include the genome database wFleaBase, which currently contains functions to search and extract information from expressed sequenced tags, genome survey sequences and full genome sequencing projects. This new database is built primarily from core components of the Generic Model Organism Database project, and related bioinformatics tools.

Summary

Over the coming year, preliminary genetic maps and the nearly complete genomic sequence of Daphnia pulex will be integrated into wFleaBase, including gene predictions and ortholog assignments based on sequence similarities with eukaryote genes of known function. wFleaBase aims to serve a large ecological and evolutionary research community. Our challenge is to rapidly expand its content and to ultimately integrate genetic and functional genomic information with population-level responses to environmental challenges. URL: http://wfleabase.org/ webcite.