DRSC announces launch of FlyPrimerBank online resource

The DRSC is pleased to announce the launch of FlyPrimerBank.

FlyPrimerBank is built around a database of three precomputed qPCR primer pairs per Drosophila gene. Online search output includes information about the primer pairs and when available, validation test results from our group or the community at large.

For details please see our paper, just out in the journal G3. You can also check out the documentation page.

Important for RNAi studies, FlyPrimerBank can report overlap between the primers and RNAi reagents in public collections. This helps you avoid choosing primers that could amplify the reagent.

As always, your feedback on the online resource is welcome.

FlyPrimerBank also makes it possible for you to indicate which qPCR primers in FlyPrimerBank have or have not worked for them, or to upload the sequences of good primer pairs not already in the database.

With your help, the utility of the resource will further increase over time.

UP-TORR. A new tool from the DRSC. Find RNAi reagents--using today's information!

The DRSC has launched a new tool! 

And a corresponding paper is now out in the journal Genetics.

Hu Y, Roesel C, Flockhart I, Perkins L, Perrimon N, Mohr S. UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents. Genetics. 2013 Jun 21. PMID: 23792952.

UP-TORR, named for "Updated Targets of RNAi Reagents" checks daily for new updates to fly gene annotations and RNAi reagent collections (including TRiP, NIG-Japan and VDRC RNAi fly stocks). This lets you view the most updated interpretation of the gene-to-RNAi-reagent relationship.

Why does this matter? Because gene annotations change--sometimes a lot--over time, changing the interpretation of on-targets and off-targets of a reagent.

Please check out our paper to learn more. We also have a help page and a video demo online. As always, feedback on the online tool is welcome.

On Orthologs, GWAS and Fly Models of Disease

A nice mention of the DRSC Integrative Ortholog Prediction Tool (DIOPT) (Hu et al. in BMC Bioinformatics) appeared recently in a Current Biology dispatch highlighting a Drosophila study investigating genes related to Restless Leg Syndrome.

Shaw & Duntley "Neurological Disorders: Towards a Mechanistic Understanding of Restless Leg Syndrome" Current Biology 22(12).

The study highlighted in the dispatch (Freeman et al. "Sleep fragmentation and motor restlessness in a Drosophila model of restless leg syndrome" Current Biology 22:1142-1148") takes human genome-wide association study (GWAS) data into a model system for functional characterization.

Shaw & Duntley state that "one of the most compelling aspects of the approach of Freeman et al. is the successful use of a model system to functionally characterize a susceptibility gene that was original identified in human genome-wide association studies" and that "the use of model systems to functionally characterize genes identified with genome-wide association studies is a move in the right direction."

At the DRSC, we are excited to see that our bioinformatics tools, as well as our RNAi reagents for cells and in vivo, can have a positive impact on the use of Drosophila to study human disease-related genes and develop disease models.

DRSC's DIOPT and DIOPT-DIST

Sneak peak for blog readers: Our new ortholog-related tools DIOPT and DIOPT-DIST are available online and a provisional version of the paper describing the tools is also available at BMC Bioinformatics. As always, your feedback on our web-based tools is welcome!