Online Tools and Databases
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Quick direct links:
iProteinDB - post translational modification tool
DIOPT ortholog search
Gene Lookup data & reagent search
UP-TORR RNAi reagent search
TRiP RNAi fly stock batch query
RSVP in vivo fly RNAi data
TRiP sgRNA fly stock nomination
Find CRISPRs sgRNA designs
Gene2Function (G2F)
Molecular Interaction Search Tool (MIST)
Search and Nominate genes for TRiP-CRISPR fly stocks
Nominate genes for CRIMIC production
find genes> | find reagents> | analyze data> | mine & visualize data |
DIOPT, DIOPT-DIST
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UP-TORR, RSVP
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HRMA
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SignedPPI, DirectedPPI, InsulinNet, MIST
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If you want to ... | We recommend ... |
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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 | |
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
. 10/11/2016. “
Featured online tool publication
- FlyPrimerBank: an online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents.” G3 (Bethesda), 3, 9, Pp. 1607-16.Abstract. 2013. “
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
- in vivo fly RNAi data at RSVP
- DRSC RNAi cell screen data at Screen Summary or Gene Lookup
- individual datasets on our Publications page (choose Dataset or data portal)
- expression data from modENCODE and others (DGET)
- basic info on TRiP fly stocks -- batch query (TRiP batch query)
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.