Fly links

Fly Links

In June 2015 a fly resource list was set up on the FlyWiki which includes all the below links. We therefore no longer update this page and refer to that list instead.

Drosophila outreach | Drosophila stock centres | News, meeting, conferences | Genome and transcriptome expression databases | Proteome and protein expression databases | Interactome databases | Transcription factor databases | Gene analysis tools | Drosophila tools and resources | Genome and proteome in silico analysis tools | Drosophila protocols | Drosophilia services | Plasmid depositories and gene libraries |

Drosophila outreach and science communication

  • FlyMove – FlyMove is an internet resource to study the development of the fruit fly Drosophila melanogaster, aimed at university students and teachers of developmental biology classes. It provides a variety of images, movies and interactive Shockwaves, which will facilitate the understanding of complex developmental processes.
  • droso4schools – a webpage accompanying free-for-download biology school lessons using Drosophila as a modern teaching tool to convey curriculum-relevant topics

Drosophila stock centres

  • Bloomington Drosophila stock center – A very large depository of different Drosophila stocks, made worldwide, is available and can be ordered from Bloomington. In 2010, the collection held 30,812 stocks at the end of the year, and distributed approximately 196,930 subcultures during the year.
  • DGRC Kyoto Stock Center – The Drosophila Genetic Resource Center (DGRC) collects and distributes Drosophila stocks from laboratories all over the world.
  • DrosDel Drosophila isogenic Deficiency Kit – The objectives of this project are to develop and distribute new stocks of wide utility to researchers and to support a thematic network of Drosophila researchers.
  • NIG Fly Stocks (RNAi stocks) – This Drosophila stock center is different to Bloomington and DGRC Kyoto. A comprehensive RNAi-mutant fly bank, which has been constructed to provide tools for better understanding of gene functions, genetic networks, screening for new genes and so on. Stocks can be ordered.
  • VDRC (Vienna Drosophila RNAi Stock Center) – The Vienna Drosophila RNAi Center (VDRC) exploits, further develops and distributes the Drosophila transgenic RNAi library generated by the Dickson group. With over 85% of the Drosophila genome covered, this promises to be a powerful method to assign functions to known and newly-annotated genes from the genome sequencing effort.
  • TRiP (Transgenic RNAi project) – Transgenic RNAi project (TRiP) facility at Harvard Medical School maintains the entire collection of TRiP stocks for people wishing to screen the lines en masse. The TRiP screening facility provides the space and equipment to carry out a complete survey of the current set of TRiP stocks. Bloomington stock center is regularily updated with new TRiP stocks.
  • The Flytrap ProjectDrosophila proteins tagged with Green Flourescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion. This scheme results in expression under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns.
  • MiMIC RMCE Lines  (line search here or heck flybase directly in the stock list of your gene of interest for all the lines with Mi{MIC} in the name). The Bellen Lab has recently generated a collection of protein trap lines containing the EGFP-FlAsH-Strep-TEV-3xFlag tag using the RMCE technique.
  • UC San Diego Stock Centre –  The Drosophila Species Stock Center (DSSC) at the University of California, San Diego is dedicated to providing a diverse array of Drosophila species to scientific researchers and educators.

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Drosophila News

  • FlyBase listings – The FlyBase maintains listings of meetings and conferences of interest to the Drosophila community. Users can also submit the name, location and dates of a conference.
  • Fly Bionet Newsgroup – BIOSCI/Bionet is a set of electronic communication forums – the bionet USENET newsgroups and parallel e-mail lists – used by biological scientists worldwide. No fees are charged for this service.
  • @fly_papers – for Twitter followers, this is the Twitterbot address that lists all fly-related papers as they hit the PubMed data base. It can also be seen under our “Fly tweets” tab.

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Drosophila genome and transcriptome expression databases

  • FlyBase – FlyBase is a comprehensive database of Drosophila genes and genomes.
  • FlyMine – FlyMine is an integrated database for Drosophila and Anopheles genomics.
  • DCPDDrosophila Core Promoter Database (DCPD) is a list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site.
  • FlyAtlas: The Drosophila gene expression atlas – FlyAtlas gives you a quick answer to the question: where is my gene of interest expressed/enriched in the adult fly? For each gene and tissue, you’re given the mRNA signal (how abundant the mRNA is), the mRNA enrichment (compared to whole flies), and the Affymetrix present call (out of four arrays, how many times it was detectably expressed).
  • FlyExpress – FlyExpress is a platform to explore expression patterns of developmentally relevant genes in Drosophila embryogenesis. It contains a unique digital library of standardised images capturing the expression of thousands of genes at different developmental stages.
  • BDGP – The BDGP database documents the patterns of gene expression in Drosophila embryogenesis.
  • Fly-FISH – The Fly-FISH database documents the expression patterns of Drosophila mRNAs at the subcellular level during early embryogenesis. A high-resolution, high-throughput fluorescence detection method is used to detect expressed mRNAs.
  • modENCODE – The National Human Genome Research Institute (NHGRI) model organism ENCyclopedia Of DNA Elements (modENCODE) Project tries to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes. modENCODE has a lot of binding site data for different proteins (ChIP-chip & ChIP-seq data), and also gene expression data (RNA-chip / RNA-seq).
  • FlyTed – The Drosophila Testis Gene Expression Database (FlyTED) contains 2,762 mRNA in situ images and ancillary data revealing the extent of expression of 819 individual genes involved in spermatogenesis in the testis of Drosophila melanogaster.
  • Flannotator – The Flannotator allows annotation of gene expression at all stages of development and tissue types (including sub cellular location) using standard Drosophila anatomy ontology. All methods of input use a controlled vocabularly to ensure data integrity.

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Drosophila proteome and protein expression database

  • PeptideAtlas – PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences.
  • PhosphoPep – PhosphoPep 2.0 provides interactive interrogation of mass spectometry-derived phosphorylation data from four different organisms. Currently there is data from the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae).
  • BrainTrap 3D – The BrainTrap database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 187 brain scans from 100 protein trap lines in the database.
  • ExPASy – The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. This server is a very comprehensive Drosophila proteomic database, which is used in the mass spectrometric referencing of identified proteins.

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Drosophila interactome databases

  • DroID – DroID (Drosophila Interactions Database) is a comprehensive gene and protein interactions database designed specifically for the model organism Drosophila. The database includes protein-protein, TF-gene, miRNA-gene, and genetic interactions.

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Drosophila transcription factor databases

  • REDfly database – REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes, and the expression patterns they direct.
  • FlyReg database – The Drosophila DNAse I footprint database has fully merged with the REDfly database to provide a one-stop portal for cis-regulatory data in Drosophila. REDfly 2.0 aims to provide a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites in Drosophila that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation.

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Drosophila gene analysis tools

  • FlyBase Blast – A genetic tool which allows Drosophila DNA sequence comparison with other fly species. Very user-friendly setup and interface.
  • FlyBase’s Genome Browser  – A very useful tool, which allows viewing Drosophila gene model features, genomic features, high throughput data, mapped features, prediction features, prior annotations, similarity proteins, similarity synteny features, similarity translated nucleotides and much more.
  • Berkeley Genome project – The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterising the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and presents up-to-date information about the annotated sequence to the research community.
  • Drosophila species genomes (DroSpeGe) – This service provides a preview of newly sequenced Drosophila genomes, with genome maps and BLAST sequence search. Genome maps include D. melanogaster genome homology, homologies to nine eukaryote proteomes, marker gene locations, and Drosophila microsatellites.
  • Ensembl’s Drosophila Genome Browser – The data displayed on the Ensembl fruit fly Drosophila melanogaster site is a compendium of data from different sources, including BDGP, FlyBase and DHGP.
  • NCBI’s Drosophila Map Viewer – Map Viewer is a powerful tool because it provides: (1) a mechanism to compare maps in different coordinate systems; (2) a robust query interface; (3) diverse options for configuring the display; (4) multiple functions to report and download maps and annotated information; (5) tools to manipulate nucleotide sequence such as ModelMaker (for constructing mRNAs from putative exon sequences); (6) connections to comprehensive data files for transfer by FTP; and (7) detailed descriptions of the objects displayed on the maps.
  • Open Genomics – Fly, worm and plant enhancer can scan any NCBI Genbank formatted genome.

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Drosophila tools and resources

  • Flybrain – An online atlas and database of the Drosophila nervous system.
  • The Interactive Fly – A cyberspace guide to Drosophila development and metazoan evolution. Virtual library of Drosophila. This directory points to internet resources for research on the fruit fly Drosophila melanogaster. Now also accompanied by a Twitter feed @interactivefly
  • Flygut – An online atlas of the Drosophila adult midgut.
  • Atlas of Drosophila development – This Atlas pictorially reviews the main events of Drosophila development. The first section gives a brief introduction to the stages of embryogenesis, followed by a composite fate map illustrating the spatial organisation of the different organ anlagen at the blastoderm stage. The remaining sections follow the development of the individual organs through embryogenesis and, in a cursory manner, postembryonic stages as well.
  • Genetic portrait– Genetic Portrait profiles model organisms such as Drosophila whose study has contributed to genetic research.
  • Learning to Fly – A poster describing phenotypic markers in Drosophila.
  • The iLab – A fun app containing pictures and descriptions of the most current mutants and species of Drosophila.
  • Virtual Fly Brain (VFB) – An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.

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Drosophila genome and proteome in silico analysis tools

  • NetPhos – The NetPhos 2.0 server produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.
  • ExPASy Tools – A very useful link containing many protein identification and characterisation tools especially useful in the field of mass spectrometry. This server offers identification and characterisation with peptide mass fingerprinting data, identification and characterisation with MS/MS data, identification with isoelectric point, molecular weight and/or amino acid composition, other prediction or characterisation tools, glycotools, DNA → Protein, similarity searches, pattern and profile searches, post-translational modification prediction and much more.
  • ProteinProspector – Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.
  • NPD – The Negative Proteome Database is populated with pair-wise protein sequence comparisons between each of the following proteomes: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Dictyostelium discoideum, Chlamydomonus reinhardti, Escherichia coli K12, Arabidopsis thaliana and Methanoscarcina acetivorans.

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Drosophila protocols

  • JOVE – The Journal of Visualized Experiments (JoVE) is a peer reviewed, PubMed-indexed video journal, containing many Drosophila related protocols and techniques.

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Drosophila services

  • BestGene, Inc– A US based company which offers partial to full service ranging from DNA preparation, embryo microinjection, screening for white+, yellow+, and/or GFP/RFP phenotypes, to balancing crosses.
  • Fly Chip – A core genomics resources for the UK Drosophila community.
  • Rainbow Transgenic Flies, Inc – A US based, research oriented, biotechnology service company. It provides services on microinjection for the fly community to make transgenic flies.

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Drosophila plasmid depositories and gene libraries

  • University of Manchester Protein Expression Core Facility – The core facility provides a comprehensive resource for high level expression and scale-up production of recombinant proteins. After an initial consultation, a small scale test expression project will be carried out to optimise conditions for maximum protein solubility, yield & integrity. This facility also offers gene mutagenesis and subcloning into the vector of choice from a large cDNA library.
  • GenScript – A US based company offering gene construction, mutagenesis and subcloning services, as well as a large array of other products and services.
  • Addgene – Addgene is a non-profit organization dedicated to making it easier for scientists to share plasmids. Addgene contains a large depository of plasmids published by scientists world wide.

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