FlyBase 102—advanced approaches to interrogating FlyBase

By Susan E. St. Pierre, Laura Ponting, Raymund Stefancsik, Peter McQuilton. Nucleic Acids Res., 2013

344 citations recorded by the source corpus.

FlyBase (http://flybase.org) is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for. Here, we demonstrate some of our more advanced searching systems and highlight some of our new tools for searching the wealth of data on FlyBase. The first section explores gene function in FlyBase, using our TermLink tool to search with Controlled Vocabulary terms and our new RNA-Seq Search tool to search gene expression. The second section of this article describes a few ways to search genomic data in FlyBase, using our BLAST server and the new implementation of GBrowse 2, as well as our new FeatureMapper tool. Finally, we move on to discuss our most powerful search tool, QueryBuilder, before describing pre-computed cuts of the data and how to query the database programmatically.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/11f4c5ee4f523af675476fa1a258fb63a7c3926a

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Citations in the corpus

• Antioxidant Role for Lipid Droplets in a Stem Cell Niche of Drosophila (2015, unknown): “…P. Bailey, Grielof Koster, Christelle Guillermier, Elizabeth M.A. Hirst, James I. MacRae, Claude P. Lechene, Anthony D. Postle and Alex P. Gould 1 SUPPLEMENTAL EXPERIMENTAL PROCEDURES Drosophila genetics Genetic elements are described in Flybase (St Pierre et al., 2014) (http://flybase.org/).”
• Olfactory responses of Drosophila suzukii females to host plant volatiles (2015, methodology): “The D. melanogaster odorant receptor orthologues extracted from FlyBase (http://www.flybase.org; St. Pierre et al., 2014) were used as a query to query (t-blastn) the D. suzukii and D. biarmipes genomes.”