HOME /

Online Tools and Databases

If you want to ... We recommend ...
Find orthologs (fly, vertebrates, worm, yeast) DIOPT [info]
G2F [info]
Find disease-related human orthologs 
(start with a gene(s) or disease term, or variant) 		DIOPT-DIST [info]
G2F [info]
MARRVEL [info]
Find RNAi fly stocks (TRiP, VDRC, NIG-Japan)
-or- find cell-based RNAi reagents (DKFZ, DRSC) 		UP-TORR [info]
Do a batch query of TRiP RNAi fly stocks TRiP Stock Lookup [info]
Find, nominate, or track TRiP sgRNA stocks for CRISPR applications sgRNA Tracking
Check if an RNAi fly stock has a reported phenotype RSVP [info]
Mine public fly cell RNAi screen data (DRSC) GeneLookup [info]
Mine public fly in vivo and cell RNA-seq data (modENCODE +) DGET [info]
Find qPCR primer designs for a fly gene(s) FlyPrimerBank [info]
Find short guide RNA (sgRNAs) for CRISPR applications in flies Find CRISPRs [info]
Evaluate sgRNAs for predicted efficiency in flies Evaluate CRISPRs [info]
Use genomic qPCR data in a high resolution melt analysis HRMA [info]
Design dsRNAs or shRNAs for fly RNAi SnapDragon [info]
View genes by list (e.g. shared pathway or domain) GLAD [info]
Look for enrichment of protein complexes in a large dataset COMPLEAT [info]
View, build, or navigate signed or directed protein networks

SignedPPI [info]
Directed PPI [info]
MIST [info]

Get quick overview of past DRSC fly cell RNAi screens with links to datasets ScreenSummary [info]
Search and visualize insulin signaling network data InsulinNet [info]
Search more than 5 million images from the Neumuller et al. cell screen on nucleolar function at HMS OMERO Image lookup for image data set at HMS OMERO
Report a software bug, make a suggestion, ask a question Bug report form

 

How to cite our suite of online tools and databases

  • Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, and Stephanie E Mohr. 10/11/2016. “FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update.” Nucleic Acids Research. Publisher's VersionAbstract
    2016_Nucl Acids Res_Hu.pdf

    The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation. In this update, we describe recent changes and additions to our website, database and suite of online tools. Recent changes reflect a shift in our focus from a single technology (RNAi) and model species (Drosophila) to the application of additional technologies (e.g. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches.

Featured online tool publication

  • Lizabeth A Perkins, Laura Holderbaum, Rong Tao, Yanhui Hu, Richelle Sopko, Kim McCall, Donghui Yang-Zhou, Ian Flockhart, Richard Binari, Hye-Seok Shim, Audrey Miller, Amy Housden, Marianna Foos, Sakara Randkelv, Colleen Kelley, Pema Namgyal, Christians Villalta, Lu-Ping Liu, Xia Jiang, Qiao Huan-Huan, Xia Wang, Asao Fujiyama, Atsushi Toyoda, Kathleen Ayers, Allison Blum, Benjamin Czech, Ralph Neumuller, Dong Yan, Amanda Cavallaro, Karen Hibbard, Don Hall, Lynn Cooley, Gregory J Hannon, Ruth Lehmann, Annette Parks, Stephanie E Mohr, Ryu Ueda, Shu Kondo, Jian-Quan Ni, and Norbert Perrimon. 2015. “The Transgenic RNAi Project at Harvard Medical School: Resources and Validation.” Genetics, 201, 3, Pp. 843-52.Abstract
    2015_Genetics_Perkins.pdf
    Supplement.pdf

    To facilitate large-scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome-scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently composed of 11,491 lines and covering 71% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated website, the RNAi Stock Validation and Phenotypes Project (RSVP, http://www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (United States), National Institute of Genetics (Japan), and TsingHua Fly Center (China).

 

Our software tools and databases can help you

  • identify orthologs among yeasts, worm, fly, and vertebrates (e.g. DIOPT)
  • identify genes in specific functional groups (GLAD)
  • identify reagents for functional genomics (e.g. UP-TORR)
  • analyze, integrate, and visualize data (e.g. COMPLEAT, SignedPPI)
  • get support for applications such as qPCR or HRMA

You can also search and view

Our 'utility tools' page includes batch search tools, common data processing tools, and more.

Click here for a full list of our bioinformatics-related publications. Or visit the individual software tool overview pages (left-hand menu) for publications, YouTube demos, and version information.

Please feel free to contact us with bug reports, suggestions, or questions. 

For more online tools relevant to the Drosophila community, we recommend visiting the FlyBase home page and the FlyBase resources wiki page. We also recommend checking out BioSharing.org, a catalog of bioinformatics databases, and the GenomeRNAi database of RNAi screen data.