Difference between revisions of "FlyBase:Drosophila Network Resources"

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(Vectors and Constructs)
(Replaced content with "=Comparative Analysises and Genome Databases= =Sequence Traces of Drosophila Genomes= =Genetic and Protein Interaction Databases= =Sequence Analysis= =Atlases, Images, and...")
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=Atlases, Images, and Videos=
 
=Atlases, Images, and Videos=
 
=Other=
 
=Other=
 
 
 
 
=Related Projects=
 
:[http://www.gmod.org/ GMOD]
 
:[http://www.geneontology.org/ Gene Ontology (GO)]
 
:[http://www.genomeknowledge.org/ Reactome]
 
:[http://www.fruitfly.org/ BDGP (Berkeley Drosophila Genome Project)]
 
:[http://dgrc.cgb.indiana.edu/ DGRC (Drosophila Genomics Resource Center)]
 
:[http://www.ou.edu/journals/dis/byissue.html DIS by issue]
 
:[http://www.flyexpress.net/ FlyExpress]
 
:[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly]
 
:[http://www.modencode.org/ modENCODE]
 
:[http://www.textpresso.org/fly/ Textpresso for Fly]
 
 
=Stock Collections=
 
===''D. melanogaster'' Collections===
 
:[http://flystocks.bio.indiana.edu/ Bloomington]
 
:[http://www.drosdel.org.uk/ DrosDel]
 
:[http://drosophila.med.harvard.edu/ Exelixis (Harvard)]
 
:[http://flypush.imgen.bcm.tmc.edu/pscreen/ GDP (Baylor)]
 
:[http://www.dgrc.kit.ac.jp/ Kyoto]
 
:[http://www.shigen.nig.ac.jp/fly/nigfly/ NIG-Fly]
 
:[http://stockcenter.vdrc.at/control/main VDRC]
 
 
===Species Collections===
 
:[http://kyotofly.kit.jp/cgi-bin/ehime/index.cgi Ehime]
 
:[https://stockcenter.ucsd.edu/info/welcome.php UC San Diego]
 
 
===Other public collections===
 
:'''Drosophila Gene Search Project'''
 
:Information about ordering P{GS} lines can be found at http://gsdb.biol.metro-u.ac.jp/~dclust/index.html
 
 
:'''Ehime Drosophila Species Stock Center of Japan'''
 
:A collection of wild-type strains of D. melanogaster and strains of some 30 species can be found at http://kyotofly.kit.ac.jp/ehime/
 
 
:'''FlyTrap Stock Collection'''
 
:GFP protein trap lines from the FlyTrap project can be obtained at Yale University, USA at http://flytrap.med.yale.edu/
 
 
:'''FlyView Stock Collection'''
 
:Enhancer trap lines from the FlyView project can be obtained at University of Muenster, Germany at http://flyview.uni-muenster.de/
 
 
:'''Kyorin-Fly'''
 
:A collection of mutant and wildtype stocks of Drosophila species, especially the Drosophila ananassae species subgroup, D. auraria complex, and D. hydei. http://kyotofly.kit.jp/cgi-bin/kyorin/index.cgi
 
 
:'''Tübingen Drosophila Stock Collection'''
 
:A list of approximately 2,000 Drosophila stocks at the Max-Planck-Institute for Developmental Biology.
 
 
:'''UC San Diego Drosophila Stock Center'''
 
:Approximately 270 different Drosophila species at University of San Diego, USA can be obtained at https://stockcenter.ucsd.edu/info/welcome.php
 
 
:'''University of Cambridge FlyProt project'''
 
:Annotations, expression patterns and sequence data for the YFP protein trap lines from the FlyProt project can be viewed on the Flannotator at http://www.flyprot.org. Stocks are available from the Kyoto Stock Center.
 
 
=Vectors and Constructs=
 
 
Genomic Insertion Collections
 
Gene Disruption Project Constructs
 
P{PZ} lacZ enhancer trap P{lacW} lacZ enhancer trap P{GT1} gene trap P{SUPor-P}  P{EP} mobile activating element P{EPg} mobile activating element P{EPgy2} mobile activating element P{Mae-UAS.6.11} mobile activating element PBac{PB} (Exelixis) PBac{GAL4D,EYFP} GAL4 binary enhancer trap Mi{ET1} GAL4 binary enhancer trap Mi{MIC} GFP gene trap, φC31 target
 
Drosophila Gene Search Project Constructs
 
P{GSV1} mobile activating element P{GSV2} mobile activating element P{GSV3} mobile activating element P{GSV6} mobile activating element P{GSV7} mobile activating element
 
Deletion Generators
 
P{XP} recombination PBac{RB} recombination PBac{WH} recombination P{RS5} recombination P{RS3} recombination PBac{5HPw[+]} recombination PBac{3HPy[+]} recombination P{wHy} hobo mobilization
 
Protein Trap Constructs
 
P{PTT-GA} GFP gene trap P{PTT-GB} GFP gene trap P{PTT-GC} GFP gene trap
 
Constructs Used for Other Collections
 
P{A92} lacZ enhancer trap P{lArB} lacZ enhancer trap P{lwB} lacZ enhancer trap P{hsneo}  P{ry11}  P{GawB} GAL4 binary enhancer trap PBac{SAstopDsRed} Tni\piggyBac mutator pP{MF3} VDRC-1 dsRNA construct collection vector pVALIUM10 TRiP-1 dsRNA construct collection vector
 
Genome Project Cloning Vectors
 
cDNA Cloning Vectors
 
pOT2  pOTB7  pCDNA-SK[+]  pCR2.1  pFLC-I  pSport1-Tag21 
 
BAC Vectors for Large Genomic Clones
 
pBACe3.6 
 
Basic Plasmid Cloning Vectors for P Transformation
 
Carnegie 20 Derivatives
 
pP{Car20} ry+t7.2 pP{Car20.1} ry+t7.2 pP{DM30} ry+t7.2
 
CaSpeR Derivatives
 
pP{CaSpeR} w+mC pP{CaSpeR-2} w+mC pP{CaSpeR-3} w+mC pP{CaSpeR-4} w+mC pP{CaSpeR-5} w+mC
 
Others
 
pP{hsneo} Tn\neoRHsp70Bb.PS pP{YES} y+mDint2 pP{W8} w+mW.hs pP{YC1.8} v+t1.8 pP{Car4} -none-
 
Plasmid Cloning Vectors with a Promoter
 
pP{CaSpeR-hs/act} Hsp70 pP{CaSpeR-hs} Hsp70 pP{CaSpeR-Hsp70/SV40} Hsp70 pP{Hsp70-CaSpeR} Hsp70 pP{W8H} Hsp70 pP{CaSpeR-act(B)} Act5C pP{CaSpeR-act(R)} Act5C pP{hsneo-act(B)} Act5C pP{hsneo-act(R)} Act5C pP{GMR} GMR (eye-specific) pP{COG} otu (oogenesis)
 
Plasmid Cloning Vectors with a Reporter Gene
 
pP{Pelican} LacZ pP{H-Pelican} LacZ pP{GreenPelican} GFP (vital reporter) pP{GreenH-Pelican} GFP (vital reporter) pP{Stinger} GFP (vital reporter) pP{H-Stinger} GFP (vital reporter) pP{RedH-Stinger} RFP (vital reporter) pP{RedH-Pelican} RFP (vital reporter) pP{YellowH-Pelican} YFP (vital reporter) pP{CaSpeR-lacZ} LacZ pP{CaSpeR-betagal} LacZ pP{CaSpeR-AUG-betagal} LacZ pP{DM79} LacZ pP{DM26} CAT pP{HZ50} LacZ pP{HZ50PL} LacZ pP{HZR} LacZ
 
Transposase Sources
 
pπ25.7wc P transposase pP{Δ2-3} P transposase pUChsΔ2-3 P transposase H{PΔ2-3} P transposase PBac{Δ2-3.Exel} P transposase pP{HBL1} hobo transposase pP{hsH\T-2} hobo transposase P{hsILMiT} Dhyd\Minos transposase P{Hsp70-PBac\T} Tni\piggyBac transposase P{Tub-PBac\T} Tni\piggyBac transposase
 
Cell Ablation Vectors and Constructs
 
pP{RMC4}  pP{UAS-RAcs2}  P{UAS-hid}  P{UAS-hid.C}  P{hs-hid}  P{UAS-Hsap\KCNJ2.EGFP}  P{UAS-NaChBac}  P{UAS-Cbβ\DT-A.I}  P{GMR-rpr.H}  P{UAS-rpr.C}  P{GMR-grim} 
 
FLP/FRT Constructs
 
pP{hsFLP}  P{70FLP}  P{hsp70-flp}  pP{neoFRT}  P{FRT(whs)}  pP{lacZ.FRT.B}  P{lacZ.Act5C.B}  pP{wg.FRT.S}  pJ35  P{ey-FLP.N}  P{ey3.5-FLP.Exel}  P{ovo-FLP.R} 
 
GAL4/UAS Cloning Vectors
 
pP{UAST}  pP{UASp}  pP{UAS-C5}  pP{GawB}  pP{WIZ} RNAi, UAS pP{PTGAL}  P{GD264}  pGaTN  pGaTB 
 
GAL4/UAS Target Constructs
 
P{UAS-lacZ.B}  P{UAS-lacZ.Hsp70}  P{UAS-lacZ.N}  P{UAS-tau-lacZ.B}  P{UAS-lacZ.NUC}  P{UAS-GFP.S65T}  P{UAS-RAcs2} Cell ablation P{AyGAL4} Mosaic analyses
 
Cell Culture Vectors
 
pMT-GAL4  pRmHa-1  pRmHa-3  pAct5CSRS  pP-Ac  pPacPL  pBLCAT3  pP{C4cat}  pSCAT0  pHGCO  p0-CAT  pcopneo 
 
Targeted Replacement Vectors and Constructs
 
pP{W25} ends-out replacement pP{W30} ends-out replacement pP{W35} ends-out replacement P{70I-SceI} source of Scer\SCEI endonuclease P{hsFLP} source of Scer\FLP1 recombinase
 
φC31 Recombination-mediated genomic insertion
 
Cloning vectors for donor element
 
Pacman1-ApR BAC cloning vector Pacman1-CmR BAC cloning vector Pacman2-ApR BAC cloning vector Pacman2-CmR BAC cloning vector Pacman2-CmR-BW BAC cloning vector pUASTattB plasmid cloning vector pwP-Ex2UASTattB plasmid cloning vector; split-white system
 
Target elements
 
PBac{y+-attP-3B} target element PBac{y+-attP-9A} target element M{wEx3-6.attP} target element, split-white system M{loxP.attP} target element M{3xP3-RFP.attP} target element M{3xP3-RFP.attP'} target element P{CaryP} target element P{UASTP2} target element
 
Integrase sources
 
M{vas-int.B} integrase source (source within genome) M{vas-int.Dm} integrase source (source within genome) M{vas-int.NLS} integrase source (source within genome) M{nos-int.NLS} integrase source (source within genome) M{nos-int.B} integrase source (source within genome) pET11φC31poly(A) template for integrase mRNA production
 
Gateway recombinational cloning vectors (promoter; tag)
 
For a complete list of Gateway vectors please see the "Data from Reference" section of this page
 
 
Vector Promoter; Tag pP{TWG} UAS; EGFP pP{TGW} UAS; EGFP pAGW Act5C (cell culture); EGFP pAWG Act5C (cell culture); EGFP pAHW Act5C (cell culture); HA1 pP{TMW} UAS; Myc pP{TWM} UAS; Myc pP{TWV} UAS; YFP pP{TVW} UAS; YFP pP{THW} UAS; HA1 pP{TWH} UAS; HA1 pP{TW} UAS; [none] pP{PWG} UASp (female germline); EGFP pP{PGW} UASp (female germline); EGFP
 
 
=Listing of all resources=
 
==Drosophila Network Resources==
 
===Comparative Analyses and Genome Databases===
 
 
    Assembly/Alignment/Annotation of 12 related Drosophila species:
 
    »Assembly/Alignment/Annotation, LBNL, USA
 
    BDGP Single Nucleotide Polymorphism (SNP) Project:
 
    »Berkeley Drosophila Genome Project, University of California, Berkeley, USA
 
    Berkeley Drosophila Genome Project (BDGP):
 
    »BDGP, University of California, Berkeley, USA
 
    BDTNP, ChIP/chip in vivo DNA binding data:
 
    »Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA
 
    CluSTr protein sequence similarity analysis of Drosophila:
 
    »CluSTr proteome analysis, EBI, UK
 
    D. pseudoobscura genome project:
 
    »Human Genome Sequencing Center, Baylor College of Medicine, USA
 
    D. simulans genome project:
 
    »Genome Sequencing Center, Washington University, USA
 
    D. yakuba genome project:
 
    »Genome Sequencing Center, Washington University, USA
 
    D.melanogaster UCSC Genome Browser Gateway:
 
    »University of California, Santa Cruz, USA
 
    DDBJ, the DNA Data Bank of Japan:
 
    »DDBJ, National Institute of Genetics, Mishima, Japan
 
    DNase I Footprint Database:
 
    »University of Manchester Bioinformatics Resources, University of Manchester, UK
 
    Drosophila Heterochromatin Genome Project (DHGP):
 
    »DHGP, Lawrence Berkeley National Laboratory, USA
 
    Drosophila melanogaster Exon Database (DEDB):
 
    »DEDB, National University of Singapore
 
    Drosophila Polymorphism Database:
 
    »Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain
 
    Drosophila Population Genomic Project (DPGP):
 
    »DPGP, University of California, Davis, USA
 
    Drosophila simulans and yakuba sequencing projects:
 
    »DPGP, University of California, Davis, USA
 
    Drosophilidae Taxonomic Database:
 
    »Drosophilidae Taxonomic Database, Japan
 
    Drosophilidae Taxonomy - Collection of Papers:
 
    »Japan Drosophila Database (JDD) on Taxonomy, Japan
 
    DRSC, Drosophila RNAi Screening Center:
 
    »DRSC, Harvard Medical School, Boston, MA, USA
 
    EMBL Nucleotide Sequence Database:
 
    »EMBL Nucleotide Sequence Database, EBI, Cambridge, UK
 
    EPD, the Eukaryotic Promoter Database:
 
    »EPD, Epalinges s/Lausanne, Switzerland
 
    euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila:
 
    » euGenes, Indiana University, USA
 
    EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences
 
    »NINDS, NIH, Bethesda MD, USA
 
    FLIGHT, Fly database for the Integration of Genomic and High-Throughput data:
 
    »FLIGHT Database, Ludwig Institute for Cancer Research, London, UK
 
    FlyAtlas, the Drosophila adult gene expression atlas:
 
    »FlyAtlas, University of Glasgow, UK
 
    FlyMine, an integrated database for Drosophila & Anopheles genomics:
 
    »University of Cambridge, United Kingdom
 
    FlyPhenomics, phenotypic differences between species of the D. melanogaster subgroup:
 
    »FlyPhenomics, Paris, France
 
    FlySNP Project:
 
    »FlySNP, Austrian Academy of Sciences, Austria
 
    GenBank,the NIH genetic sequence database:
 
    »GenBank, NCBI, Bethesda, MD USA
 
    GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:
 
    »GenomeRNAi, DKFZ, Heidelberg, Germany
 
    GEO, NCBI's Gene Expression Omnibus:
 
    »GEO, NCBI, Bethesda, MD USA
 
    GPCRDB, information system for G protein-coupled receptors (GPCRs):
 
    »GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership
 
    Homophila, Human Disease to Drosophila Gene Database:
 
    » Homophila, San Diego, USA
 
    InParanoid, Eukaryotic Ortholog Groups:
 
    »InParanoid, Karolinska Institute, Sweden
 
    InterPro protein domain analysis of Drosophila:
 
    »InterPro proteome analysis, EBI, UK
 
    MANTiS a phylogenetic framework for multi-species genome comparisons:
 
    »MANTiS, Université Libre de Bruxelles, Belgium
 
    MEROPS, an information resource for peptidases:
 
    »MEROPS, The Sanger Institute, Cambridge, UK
 
    miRBase, microRNA data:
 
    »miRBase, The Sanger Institute, Cambridge, UK
 
    miRNA, Target Gene Prediction:
 
    »miRNA - Target Prediction, EMBL, Heidelberg, Germany
 
    MitoDrome, Drosophila melanogaster nuclear genes encoding for mitochondrial proteins:
 
    »MitoDrome, Bari, Italy
 
    Mitotic Spindle Assembly Database:
 
    »Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA
 
    NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing:
 
    »National Human Genome Research Institute, Bethesda, MD, USA
 
    Panther protein classification system:
 
    »Panther Protein Classification System, Applied Biosystems & Celera, USA
 
    PDB, Protein Data Bank:
 
    »PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium
 
    PhospoPep - phosphorylation site data from D. melanogaster cell lines:
 
    »The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.
 
    Proteome analysis of Drosophila:
 
    »Proteome analysis, EBI, UK
 
    PubMed, Biomedical literature citations and abstracts:
 
    »PubMed, NCBI, Bethesda, MD USA
 
    REDfly, Regulatory Element Database for Drosophila:
 
    »REDfly, University at Buffalo, New York, USA
 
    Rfam, RNA families database of alignments and CMs:
 
    »Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA
 
    Sebida, Sex Bias Database:
 
    »Sebida, MPI Martinsried, Germany
 
    TaxoDros, the database on Taxonomy of Drosophilidae:
 
    »TaxoDros, University of Zurich, Switzerland
 
    The Drosophila Transcription Factor Database:
 
    »FlyTF.org, MRC Cambridge, UK
 
    The McGill Drosophila melanogaster Genome Project:
 
    »McGill Drosophila Genome Project, Canada
 
    TRANSFAC, A database of transcription factors and their binding sites:
 
    »TRANSFAC, Braunschweig, Germany
 
    TransTerm, a Translational Signal Database:
 
    »TransTerm, Dunedin, New Zealand
 
    UniProtKB, a comprehensive catalog of information on proteins:
 
    »UniProtKB, The UniProt Consortium
 
    Whole genome comparative analysis of D. melanogaster and D. pseudoobscura:
 
    »Whole genome analysis, LBNL, USA
 

Revision as of 17:53, 13 February 2014

Comparative Analysises and Genome Databases

Sequence Traces of Drosophila Genomes

Genetic and Protein Interaction Databases

Sequence Analysis

Atlases, Images, and Videos

Other