Difference between revisions of "FlyBase:Drosophila Online Resources"
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==General== | ==General== | ||
| − | * <b>Rfam</b>, RNA families | + | * <b>Rfam</b>, A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements. (last updated 2017):<br />[http://rfam.xfam.org/ Rfam, EMBL-EBI, Hingston, UK] |
| − | * <b>RNAcentral</b>, | + | * <b>RNAcentral</b>, Integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases (last updated 2017):<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hingston, UK] |
| + | |||
==miRNA== | ==miRNA== | ||
===General=== | ===General=== | ||
Revision as of 14:26, 27 June 2017
Atlases, Images and Videos
- Atlas of Drosophila Development, An Atlas following the main events of embryogenesis and post-embryonic development:
Volker Hartenstein and Interactive Fly, Bethesda, MD, USA - BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm:
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA - BrainTrap, A collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project:
Armstrong Lab, University of Edinburgh, Edinburgh, UK - CSIRO Anatomical Atlas of Flies:
CSIRO Entomology, Australia - FlyBase Maps, A collection of illustrated and electron micrograph maps of polytene chromosomes for the 12 originally sequenced Drosophila species:
FlyBase Maps - FlyCircuit, a Database of Drosophila Brain Neurons:
FlyCircuit, National Tsing Hua University, Taiwan - FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany - FlyPNS, D. melanogaster embryonic and larval peripheral nervous system:
FlyPNS, UMPC, Paris, France and Columbia University, NY, USA - FlyView, a Drosophila Image Database:
FlyView, Muenster, Germany - GETDB, a Gal4 enhancer trap database:
GETDB, Kyoto Institute of Technology, Kyoto, Japan - Interactive Maps: four maps displaying markers and lineages of D. melanogaster neuroblasts, glial cells, and interneurons:
Interactive Maps, Institut fur Genetik, Johannes Gutenberg University, Mainz, Germany - Jove, videos of experimental techniques:
Jove, Journal of Visualized Experiments, USA - Learning to Fly, a poster showing photographs of commonly used marker phenotypes in D. melanogaster:
Genesis (Journal), Wiley Online Library - PeptideAtlas, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments:
Seattle Proteome Center, Seattle, Washington, USA - Virtual Fly Brain - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:
Virtual Fly Brain, Edinburgh and Cambridge, UK
CRISPRs and TALENs
- CCTop CRISPR/Cas9 optimum target finder:
Center for Organismal Studies, Heidelberg University, Heidelberg, DE - CHOPCHOP CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:
Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA - CRISPOR Model organism gRNA design tool:
TEFOR, Gif-sur-Yvette, France - CRISPR/Cas Web Resources Web Resources for design and planning of CRISPR/Cas9 studies:
IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA - CRISPR-ERA A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:
Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA - CRISPR Genome Engineering Resources CRISPR Design Tool:
Zhang Lab, MIT, Boston, MA, USA - CRISPR fly design -- reagents, protocols, and results from fly CRISPR/Cas experiments:
Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK - CRISPRscan Novel scoring algorithm for selecting sgRNAs
Giraldez Lab, Yale University, New Haven, CT, USA - DRSC CRISPR Efficiency Tool for Assessment of Designs:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - DRSC Finding CRISPRs, Drosophila CRISPR gRNA design search tool:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - E-CRISP, Design of CRISPR Constructs:
DKFZ/Boutros lab, Heildelberg, Germany - E-TALEN, Design of TALEN Constructs:
DKFZ/Boutros lab, Heildelberg, Germany - flyCRISPR, Resource Site:
O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA - flyCRISPR, Optimal Target Finder:
O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA - Genome Engineering by CRISPR/Cas9 in Drosophila:
NIG/FLY/Ueda lab, Mishima, Japan - Mojo Hand, A TALEN Design Tool:
Ekker lab, Mayo Clinic, Rochester, MN, USA - OXfCRISPR, Oxford Fly CRISPR Resources:
Liu lab, University of Oxford, Oxford, UK - SIFTED, Specificity Inference for TAL Effector Design:
Bulyk Lab, Harvard Medical School, Boston, MA, USA - TALengineering.org, A Comprehensive Resource for Engineered TAL Effector Technology:
Ekker lab, Joung Lab, MGH, Boston, USA - ZiFiT Targeter, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:
MGH and Harvard Medical School, Boston, MA
Data Repositories
- Array Express - Functional Genomics Data:
Array Express, EMBL-EBI, Hinxton, UK - Berkeley Drosophila Genome Project (BDGP):
BDGP, University of California, Berkeley, USA - DDBJ, the DNA Data Bank of Japan:
DDBJ, National Institute of Genetics, Mishima, Japan - EMBL-EBI, The European Bioinformatics Institute:
EMBL-EBI, Hinxton, UK - ENA, European Nucleotide Archive:
ENA, European Nucleotide Archive, EMBL-EBI, Hinxton, UK - Ensembl Genome Browser:
EMBL-EBI, Hinxton, UK - Gene Disruption Project (GDP):
GDP, Baylor College of Medicine, Texas
Schematic drawings of Transposons - GenBank,the NIH genetic sequence database:
GenBank, NCBI, Bethesda, MD USA - GEO Datasets, Gene Expression Omnibus:
NCBI, Bethesda, MD USA - NCBI, National Center fo Biotechnology Information:
Bethesda, MD USA - NCBI Map Viewer, A genome view of Drosophila melanogaster:
NCBI, Bethesda, MD USA - PubMed, Biomedical literature full-text archive:
PubMed, NCBI, Bethesda, MD USA - PubMed Central, Biomedical literature citations and abstracts:
PubMed Central, NCBI, Bethesda, MD USA - SRA, Sequence Read Archive:
SRA, NCBI, Bethesda, MD, USA - UCSC Genome Browser Gateway - D. melanogaster:
UCSC Genome Browser, UC Santa Cruz, USA
Drosophila Genomes Data and Metadata
- DroSpeGe, a view of Drosophila genome data, with genome maps and BLAST sequence search, for 12 species:
Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA - List of Drosophila reference genome assemblies at FlyBase, NCBI and UCSC. File:DrosophilaGenomeAssemblies.xls (spreadsheet) Updated June 17, 2015
- D. albomicans Genome:
D. albomicans Organism Overview, NCBI, USA
D. albomicans Genome Assembly Report, NCBI, USA
D. albomicans Genome Assembly Report, ENA, UK - D. americana Genome:
D. americana Organism Overview, NCBI, USA
D. americana Genome Assembly Report, NCBI, USA
D. americana Genome Assembly Report, ENA, UK - D. ananassae Genome:
D. ananassae Organism Overview, NCBI, USA
D. ananassae Genome Assembly Report, NCBI, USA
D. ananassae Genome Assembly Report, ENA, UK - D. arizonae Genome:
D. arizonae Organism Overview, NCBI, USA
D. arizonae Genome Assembly and Annotation Report, NCBI, USA
D. arizonae Genome Assembly Report, ENA, UK - D. biarmipes Genome:
D. biarmipes Organism Overview, NCBI, USA
D. biarmipes Genome Assembly Report, NCBI, USA
D. biarmipes Genome Assembly Report, ENA, UK - D. bipectinata Genome:
D. bipectinata Organism Overview, NCBI, USA
D. bipectinata Genome Assembly Report, NCBI, USA
D. bipectinata Genome Assembly Report, ENA, UK - D. busckii Genome:
D. busckii Organism Overview, NCBI, USA
D. busckii Genome Assembly Report, NCBI, USA
D. busckii Genome Assembly Report, ENA, UK - D. erecta Genome:
D. erecta Organism Overview, NCBI, USA
D. erecta Genome Assembly Report, NCBI, USA
D. erecta Genome Assembly Report, ENA, UK - D. elegans Genome:
D. elegans Organism Overview, NCBI, USA
D. elegans Genome Assembly Report, NCBI, USA
D. elegans Genome Assembly Report, ENA, UK - D. eugracilis Genome:
D. eugracilis Organism Overview, NCBI, USA
D. eugracilis Genome Assembly Report, NCBI, USA
D. eugracilis Genome Assembly Report, ENA, UK - D. ficusphila Genome:
D. ficusphila Organism Overview, NCBI, USA
D. ficusphila Genome Assembly Report, NCBI, USA
D. ficusphila Genome Assembly Report, ENA, UK - D. grimshawi Genome:
D. grimshawi Organism Overview, NCBI, USA
D. grimshawi Genome Assembly Report, NCBI, USA
D. grimshawi Genome Assembly Report, ENA, UK - D. kikkawai Genome:
D. kikkawai Organism Overview, NCBI, USA
D. kikkawai Genome Assembly Report, NCBI, USA
D. kikkawai Genome Assembly Report, ENA, UK - D. melanogaster Genome:
D. melanogaster Organism Overview, NCBI, USA
D. melanogaster Genome Assembly Report, NCBI, USA
D. melanogaster Genome Assembly Report, ENA, UK - D. miranda Genome:
D. miranda Organism Overview, NCBI, USA
D. miranda Genome Assembly Report, NCBI, USA
D. miranda Genome Assembly Report, ENA, UK - D. mojavensis Genome:
D. mojavensis Organism Overview, NCBI, USA
D. mojavensis Genome Assembly Report, NCBI, USA
D. mojavensis Genome Assembly Report, ENA, UK - D. navojoa Genome:
D. navojoa Organism Overview, NCBI, USA
D. navojoa Genome Assembly Report, NCBI, USA
D. navojoa Genome Assembly Report, ENA, UK - D. persimilis Genome:
D. persimilis Organism Overview, NCBI, USA
D. persimilis Genome Assembly Report, NCBI, USA
D. persimilis Genome Assembly Report, ENA, UK - D. pseudoobscura Genome:
D. pseudoobscura Organism Overview, NCBI, USA
D. pseudoobscura Genome Assembly Report, NCBI, USA
D. pseudoobscura Genome Assembly Report, ENA, UK - D. rhopaloa Genome:
D. rhopaloa Organism Overview, NCBI, USA
D. rhopaloa Genome Assembly Report, NCBI, USA
D. rhopaloa Genome Assembly Report, ENA, UK - D. sechellia Genome:
D. sechellia Organism Overview, NCBI, USA
D. sechellia Genome Assembly Report, NCBI, USA
D. sechellia Genome Assembly Report, ENA, UK - D. simulans Genome:
D. simulans Organism Overview, NCBI, USA
D. simulans Genome Assembly Report, NCBI, USA
D. simulans Genome Assembly Report, ENA, UK - D. suzukii Genome:
D. suzukii Organism Overview, NCBI, USA
D. suzukii Genome Assembly Report, NCBI, USA
D. suzukii Genome Assembly Report, ENA, UK
D. suzukii SpottedWingFlyBase The Spotted Wing Drosophila Project, UC Davis and Oregon State University, USA - D. takahashii Genome:
D. takahashii Organism Overview, NCBI, USA
D. takahashii Genome Assembly Report, NCBI, USA
D. takahashii Genome Assembly Report, ENA, UK - D. virilis Genome:
D. virilis Organism Overview, NCBI, USA
D. virilis Genome Assembly Report, NCBI, USA
D. virilis Genome Assembly Report, ENA, UK - D. willistoni Genome:
D. willistoni Organism Overview, NCBI, USA
D. willistoni Genome Assembly Report, NCBI, USA
D. willistoni Genome Assembly Report, ENA, UK - D. yakuba Genome:
D. yakuba Organism Overview, NCBI, USA
D. yakuba Genome Assembly Report, NCBI, USA
D. yakuba Genome Assembly Report, ENA, UK]
Gene Expression Databases and Tools
- BDGP in situ, Patterns of gene expression in Drosophila embryogenesis:
Gene expression database, BDGP, University of California, Berkeley, USA - BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA - BGee Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).
SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland - Flannotator, Annotation of Gene Expression:
FlyAnnotator, University of Cambridge, UK - FlyAtlas2, for exploring how genes are expressed in the tissues of D. melanogaster:
FlyAtlas2, University of Glasgow, Glasgow, UK - FlyEx, a Database of Segmentation Gene Expression in Drosophila:
FlyEx, St. Petersburg State Polytechnical University, Russia - FlyExpress, an Expression Pattern Search Engine:
FlyExpress, Arizona State University, USA - Fly-FISH, A Database of Drosophila Embryo mRNA Localizaton Patterns:
Fly-FISH, University of Toronto, Toronto, Canada - FlyGut-seq, a transcriptomic resource that complements the original Flygut website:
Buchon Lab, Cornell University, Ithaca, NY, USA - FlyLight, Expression Patterns of GAL4 Driver Lines:
HHMI, Janelia Farms Research Campus - FlyOde, FLY Organ Developmental Network:
FlyOde, Bogazici University, Istanbul, Turkey - flytrap, a database of P{GAL4} enhancer traps and their expression in brains:
flytrap, University of Edinburgh, UK - Gene Expression Levels by Cell Line (based on modENCODE data):
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - GEO Profiles, Gene Expression Omnibus:
GEO, NCBI, Bethesda, MD USA - GEO Profiles, Gene Expression Omnibus:
GEO, NCBI, Bethesda, MD USA - MidgutAtlas, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:
Dow laboratory, University of Glascow, Scotland, UK - RNAMiner, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:
Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA
Gene Groups
- FlyBase Gene Groups, Manually curated reports on functionally related genes, based on the literature:
Gene group list, FlyBase - GLAD, an Online Database of Gene List Annotations for Drosophila:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - Interactive fly, Drosophila genes listed by biochemical function:
Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA - Interactive fly, Maternally transcribed genes:
Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA - Interactive fly, Zygotically transcribed genes:
Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA - KEGG BRITE, Functional hierarchies and binary relationships of biological entities:
KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan - UCSC D. melanogaster Gene Sorter, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:
UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA
General Bioinformatics Tools
- Bioconductor, Open Source Software for Bioinformatics:
Fred Hutchinson Cancer Research Center, Seattle, USA - BioMart, Data Warehouse:
BioMart, EMBL-EBI, OICR, SRSI - Bioz, Insights and recommendations for products, equipment and assays:
Palo Alto, CA, USA - Cytoscape -- Network Data Integration, Analysis, and Visualization in a Box:
Cytoscape, Cytoscape Consortium, Canada, France, and USA - DNA & Protein Work List, A list of tools aggregated by the Prokop Lab:
http://www.prokop.co.uk/Links/tools.html - FlyMine, an Integrated Database for Drosophila and Anopheles Genomics:
University of Cambridge, United Kingdom - FlyNet, a network prioritization server for Drosophila melanogaster biology:
NetBioLab, Yonsei University, Seoul, Korea - Galaxy: Open Source Bioinformatics Tools:
Galaxy, Penn State, PA USA and Emory University, GA USA - GSEA, Gene Set Enrichment Analysis:
GSEA, Broad Institute, Cambridge, MA, USA
Genome Sequencing Projects
- D. pseudoobscura genome project:
D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA - D. simulans genome project:
D. simulans White 501 Genome Sequencing Center, Washington University, USA - D. yakuba genome project:
D. yakuba Genome Sequencing Center, Washington University, USA - D. simulans and yakuba sequencing projects:
DPGP, University of California, Davis, USA
Human Disease: Drosophila Models and Orthologous Genes
- Bloomington Stock Center, Drosophila and Human Disease page:
Bloomington Stock Center, Bloomington, IN, USA - DIOPT-DIST, Disease-related Ortholog Tool:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - Drosophila as a Model for Human Diseases:
Interactive Fly, Bethesda, MD, USA - Drosophila Models of Human Disease, a blog by Stephanie Mohr and Annette Parks:
flydiseasemodels.blogspot.com/ - FlyNet Human Disease Prioritization:
NetBioLab, Yonsei University, Seoul, Korea - HuDis, high confidence human disease gene - fly gene ortholog pairs:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - MORPHIN, Model ORganism Projected on a Human Integrated gene Network:
MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA. - NeuroGeM, A knowledgebase of genetic modifiers in neurodegenerative diseases:
CHiBi, The University of British Columbia, Vancouver, BC, Canada
Interaction and Pathway Databases
- BioGRID, The General Repository for Interaction Datasets:
BioGRID, Mount Sinai Hospital, Toronto, Canada - COMPLEAT, protein COMPLex Enrichment Analysis Tool:
COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA - DAPPER, database for protein-protein interactions:
DAPPER, University of Cambridge, Cambridge, UK - DPiM, Drosophila Protein interaction Map:
DPiM, Harvard University Medical School, Boston, MA, USA - DroID, Drosophila Interactions Database:
Drosophila Interaction Database, Detroit, USA - Drosophila PIMRider, Drosophila Protein Interaction Map:
Drosophila PIMRider, Hybrigenics, Paris, France - FlyCyc -- Curated Drosophila melanogaster Pathways:
FlyCyc, Harvard University, Cambridge, USA - FlyNet Gene Prioritization:
NetBioLab, Yonsei University, Seoul, Korea - FlyOde, FLY Organ Developmental Network:
FlyOde, Bogazici University, Istanbul, Turkey - FlyReactome -- a Curated Knowledgebase of Drosophila melanogaster Pathways:
FlyReactome, University of Cambridge, Cambridge, UK - IM Browser, Drosophila Interactions Database:
IM Browser, Wayne State University, Detroit, MI, USA - IntAct, Molecular Interaction Database:
IntAct, EMBL-EBI, Hinxton, UK - KEGG -- Kyoto Encyclopedia of Genes and Genomes:
KEGG, Kyoto, Japan - Reactome Pathway Database:
Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA - SignedPPI, Searchable Database of Known and Predicted Protein-protein Interactions:
DRSC, Harvard Medical School, Boston, MA, USA - STRING, Known and Predicted Protein-Protein Interactions
STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany - WikiPathways, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:
WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands
Laboratory Resources
- Laboratory Manual of Drosophila:
PDF, Chippindale, A. et al., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA
Miscellaneous
- Bionet Archives, a collection of bionet USENET newsgroups and parallel e-mail lists regarding Drosophila:
Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA - DOR, Database of Olfactory Receptors:
DOR, NCBS, Bangalore, India, AIST, Tokyo, Japan - Drosophila App, A mobile application developed by Genesee for use in fly research:
iTunes | Android - Drosophila Information Service:
DIS, Norman, Oklahoma, USA - Fly Labs and References, a large list of fly labs and recent publications:
Interactive Fly, Bethesda, MD, USA - FlyTree, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project:
FlyTree, USA - GenAge -- The Ageing Gene Database:
Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK - Gene Lookup, Gene and Reagent Lookup:
Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA - IGTRCN, Insect Genetic Technologies Research Coordination Network:
IGTRCN, University of Maryland, Rockville, MD, USA - Interactive Fly, A cyberspace guide to Drosophila development and metazoan evolution
Interactive Fly, Bethesda, MD, USA - Jfly, a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:
Jfly, University of Tokyo, Japan - Manchester Fly Facility, Outreach resources - A compendium of information on Drosophila melanogaster as a model organism:
University of Manchester, Manchester, UK - 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 - Multiplex Fluorescent mRNA In Situ Hybridization, information on how to perform multiplex fluorescent mRNA in situ hybridization on Drosophila embryos:
Bier and McGinnis Labs, UCSD, San Diego, California, USA - 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. - What's hot today: Current papers in developmental biology and gene function:
Interactive Fly, Bethesda, MD, USA - The WWW Virtual Library--Drosophila:
Drosophila Virtual Library
Non-coding (ncRNA) Databases and Tools
General
- Rfam, A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements. (last updated 2017):
Rfam, EMBL-EBI, Hingston, UK - RNAcentral, Integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases (last updated 2017):
RNAcentral, EMBL-EBI, Hingston, UK
miRNA
General
- miRBase, A searchable database of published miRNA sequences and annotation (last updated 2014):
miRBase, University of Manchester, UK
- NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.
- Tools4miRs, Manually curated platform gathering methods for the broadly-defined miRNA analysis (last updated 2017):
Tools4miRs, Polish Academy of Sciences and University of Warsaw, Warsaw, Poland
miRNA Target Prediction
- DIANA microT-CDS, MicroRNA Target Prediction (last updated 2014):
DIANA microT-CDS, DIANA LAB, Athens, Greece - MicroCosm Targets, Computationally predicted targets for microRNAs across many species (last updated 2007):
MicroCosm Targets, EMBL-EBI, Hinxton, UK - microRNA.org, Predicted microRNA targets & target downregulation scores (last updated 2007):
microRNA.org, Memorial Sloan-Kettering Cancer Center, New York, NY, USA - MinoTar, Predict microRNA Targets in Coding Sequence (last updated 2010):
MinoTar, DRSC, Harvard Medical School, Boston, MA, USA - miRNA - Target Gene Prediction (last updated 2005):
miRNA - Target Prediction, EMBL, Heidelberg, Germany - miRNA_Targets (last updated 2011):
miRNA targets on full length mRNAs, Deakin University, Victoria, Australia - TargetScanFly, Prediction of microRNA targets (last updated 2012):
TargetScanFly, Whitehead Institute and MIT Dept. of Biology, Cambridge, MA, USA
Validated miRNA Targets
- DIANA TarBase, MicroRNA Target Database (last updated 2014):
DIANA TarBase, DIANA LAB, Athens, Greece - miRecords, A database of experimentally validated miRNA targets curated from literature (last updated 2009):
miRecords, University of Minnesota, Minneapolis, MN, USA - miRTarBase, Experimentally Validated microRNA-target Interactions Database (last updated 2015):
miRTarBase, ISBLab, Hsinchu, Taiwan - miRTex, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):
miRTex, University of Delaware, Newark, DE, USA
Comparative miRNA Analysis
- CoGemiR, Comparative Genomics Analysis of MicroRNA (last updated 2008):
CoGemiR, Telethon Institute of Genetics and Medicine, Naples, Italy - microRNAviewer, A global view of homologous miRNA genes in many species (last updated 2012):
microRNAviewer, Tel Aviv University, Tel Aviv, Israel
rRNA
- SILVA, High quality ribosomal RNA databases (last updated 2016):
SILVA, Max Planck Institute for Marine Microbiology and Jacobs University, Bremen, Germany
tRNA
- GtRNAdb, tRNAscan-SE analysis of complete genomes:
GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA - tRFdb, A relational database of Transfer RNA related Fragments:
tRFdb, Dutta lab, University of Virginia, Charlottesville, VA, USA
snoRNA
- snOPY, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:
snOPY, University of Miyazaki, Japan
SRP
- SRPDB, Signal Recognition Particle Database:
SRPDB, University of Texas Health Science Center, San Antonio, USA
Ontology Resources
- AmiGO 2, tools for searching and browsing the Gene Ontology database:
AmiGO 2, Berkeley Bioinformatics Open-source Projects, USA - BioPortal, a biomedical ontologies repository and browser:
BioPortal, The National Center for Biomedical Ontology, USA - Disease Ontology, ontology of disease terms:
Disease Ontology - Gene Ontology Consortium
Gene Ontology Consortium - GOrilla -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:
GOrilla, Israel - OboEdit, browser for OBO ontologies:
OboEdit - The OBO Foundry, an ontology registry:
OboFoundry - Ontobee, an ontologies browser:
Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA - Ontology Lookup Service, an ontologies browser:
Ontology Lookup Service, EMBL-EBI, Hinxton, UK - Protege, browser for OWL ontologies:
Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA - QuickGO, a browser for Gene Ontology terms and annotations:
QuickGO, EMBL-EBI, Hinxton, UK
Orthology Predictions
- Compara, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.
Ensembl, Hinxton, UK - DIOPT, DRSC Integrative Ortholog Prediction Tool
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - DIOPT-DIST: DIOPT Diseases and Traits, DRSC Disease Gene Query Tool:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - EggNOG, A database of orthologous groups and functional annotation:
Computational Biology Group, EMBL, Heidelberg, Germany - Homologene, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.
NCBI, Bethesda, MD, USA - Inparanoid, InParanoid: ortholog groups with inparalogs
Stockholm Bioinformatics Centre, Stockholm, Sweden - Isobase, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.
MIT, Cambridge, MA, USA - OMA Browser, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.
Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158 - OrthoDB, The Hierarchical Catalog of Orthologs
Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland - OrthoMCL, Ortholog Groups of Protein Sequences
EuPathDB - PANTHER, PANTHER Classification System
Thomas Lab, University of Southern California, Los Angeles, CA, USA - PhylomeDB, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)
Comparative Genomics Groups at CRB, Barcelona, Spain - Roundup, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.
Wall lab, Stanford University, Palo Alto, CA, USA - TreeFam, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.
EMBL-EBI, Hinxton, UK
Phylogenetic Comparison Tools
- DIOPT, DRSC Integrative Ortholog Prediction Tool:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA - EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences
NINDS, NIH, Bethesda MD, USA - HomoloGene -- automated system fo constructing putative homology groups:
NCBI, Bethesda, MA, USA - InParanoid, Eukaryotic Ortholog Groups:
InParanoid, Karolinska Institute, Sweden - MANTiS, a phylogenetic framework for multi-species genome comparisons:
MANTiS, Université Libre de Bruxelles, Belgium - OrthoDB, the Hierarchical Catalog of Orthologs:
OrthoDB, University of Geneva, Switzerland - flyDIVaS, a comparative genomics database resource of Drosophila divergence and selection:
Temple University, Philadelphia, PA, USA - Vista Tools -- Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome:
Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA
Population Biology and Polymorphism Resources
- BDGP Single Nucleotide Polymorphism (SNP) Project:
Berkeley Drosophila Genome Project, University of California, Berkeley, USA - Drosophila Genetics Reference Panel:
DGRP, Baylor College of Medicine, Houston, TX and NC State University, Raleigh, NC USA - Drosophila Genetics Reference Panel 2:
DGRP2, NC State University, Raleigh, NC and Baylor College of Medicine, Houston, TX, USA - Drosophila Genome Nexus: a population genomic resource that provides D. melanogaster genomes from multiple sources
University of Wisconsin, Madison, WI, USA - Drosophila Polymorphism Database:
DPDB, Universitat Autonoma de Barcelona, Barcelona, Spain - DPGP, Drosophila Population Genomics Project:
DPGP, University of California, Davis, USA - DSPR, Drosophila Synthetic Population Resource:
DSPR, University of Kansas and UC Irvine, USA - FlySNP Project:
FlySNP, Austrian Academy of Sciences, Austria - FlyVar Project: A Database of Drosophila Genetics Variations
FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA - Global Diversity Lines: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains
Global Diversity Lines, Cornell University, Ithaca, NY, USA
Protein Analysis
- ExPASy, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:
SIB Swiss Institute of Bioinformatics, Genève, Switzerland - GPCRDB, information system for G protein-coupled receptors (GPCRs):
GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership - InterPro protein domain analysis of Drosophila:
InterPro: protein sequence analysis & classification, EBI, UK - MEROPS, an information resource for peptidases:
MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK - ModBase, Database of Comparative Protein Structure Models:
ModBase, UCSF, San Francisco, CA, USA - Panther (Protein Analysis THrough Evolutionary Relationships) 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, interactive interrogation of MS-derived phosphorylation data from 4 different organisms:
Institute for Systems Biology, Seattle, Washington, USA - ProteinProspector, a proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments:
UCSF Mass Spectrometry Facility, San Francisco, California, USA - RBPDB, the database of RNA-binding protein specificities:
RBPDB - SMART, Simple Modular Architecture Research Tool:
SMART, Protein Domain Analysis, EMBL, Heidleberg - UniProtKB, a comprehensive catalog of information on proteins:
UniProtKB, The UniProt Consortium
Public Education
- About the history of Drosophila research, An extensive collection of media pertaining to the history of fruit fly research:
Manchester Fly Facility, University of Manchester, UK - droso4schools, An online resource for school lessons using the fruit fly Drosophila:
Manchester Fly Facility, University of Manchester, UK - Drosophila & Computer Programming Game, A scratch computer game based on the Drosophila life cycle:
Manchester Fly Facility, University of Manchester, UK - Fly on the Wall, a blog by Bethany Christmann regarding fruit flies and research:
Griffith Lab, Brandeis University, Waltham, MA, USA - FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany - Manchester Fly Facility Public Resource Page:
Manchester Fly Facility, University of Manchester, UK
RNAi
- DRSC-TRiP-FGR, DRSC/TRiP Functional Genomics Resources:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - Search by gene(s) to find hits in DRSC screens:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - FlyRNAi blog, a DRSC resource concerning RNAi, cell-based assays, Drosophila cell culture, high-throughput screening, & fly biology:
flyrnai.blogspot.com - Fosmid rescue analysis tool for identification of fosmids appropriate for cross-species rescue of RNAi:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens:
GenomeRNAi, DKFZ, Heidelberg, Germany - GESS, off-target RNAi prediction:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - Predicted Off-Target Free Sequence Regions:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - RNAiCut, Automated Detection of Significant Genes from Functional Genomic Screens:
Berger Lab, MIT, Boston, MA, USA - RSVP, RNAi Stock Validation & Phenotypes:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - SnapDragon, RNAi Design:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - TRiP, Transgenic RNAi Project:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - Tsinghua Fly Center, Transgenic RNAi lines:
Center of Biomedical Analysis, Tsinghua University, Beijing, China - UP-TORR Fly, a tool for identifying updated targets of RNAi reagents:
Updated Targets of RNAi Reagents, DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA - VDRC, Vienna Drosophila Resource Center:
Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria
Sequence Analysis
- DCPD -- Drosophila Core Promoter Database, A list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site:
Kadonaga Lab, UCSD, San Diego, California, USA - EvoPrinterHD, A "High Definition" view of conserved DNA:
NINDS, NIH, Bethesda, MD, USA - FlyPrimerBank, a comprehensive qPCR primer database for Drosophila:
FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA - FGENESH, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:
Annotation of genomes, Softberry, USA - GenePalette, a tool for genome sequence visualization and navigation:
GenePalette, University of California, San Diego, USA - Genie Gene finder for Drosophila:
Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA - HRMA -- High Resolution Melt Analysis:
HRMA, DRSC, Harvard Medical School, Boston, MA, USA - MEME Suite -- Motif-based Sequence Analysis Tools:
MEME, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources - RepeatMasker:
RepeatMasker Institute for Systems Biology, Seattle, WA, USA - Splice Site Prediction for Drosophila:
Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA - Web Apollo, a collaborative genomic annotation editor:
Web Apollo, LBL, Berkeley, USA
Taxonomy
- Drosophilidae Taxonomic Database:
Drosophilidae Taxonomic Database, Japan - Drosophilidae Taxonomy -- Collection of Papers:
Japan Drosophila Database (JDD) on Taxonomy, Japan - FlyPhenomics, phenotypic differences between species of the D. melanogaster subgroup:
FlyPhenomics, Paris, France - TaxoDros, the database on Taxonomy of Drosophilidae:
TaxoDros, University of Zurich, Switzerland - Taxonomy, NCBI Taxonomy Database:
NCBI, Bethesda, MD USA
Transcription Regulation Databases and Tools
- BDTNP, ChIP/chip in vivo DNA binding data:
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA - CORE, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements:
Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel - DBD, Transcription factor prediction database:
DBD, MRC, Cambridge, UK - ElemeNT, An interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language:
Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel
- EPD, the Eukaryotic Promoter Database:
EPD, Epalinges s/Lausanne, Switzerland - Fly Factor Survey - Database of Drosophila TF DNA-binding Specificitiies:
FLy Factor Survey, UMass Medical School, Worcester, MA, USA - FlyReg, DNase I Footprint Database:
University of Manchester Bioinformatics Resources, University of Manchester, UK - i-cisTarget, An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly:
i-cisTarget, University of Leuven, Leuven, Belgium - Neural Network Promoter Prediction for Drosophila:
Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA - OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites
OnTheFly, Columbia University, USA - REDfly, Regulatory Element Database for Drosophila:
REDfly, University at Buffalo, New York, USA - The Drosophila Transcription Factor Database:
FlyTF.org, MRC Cambridge, UK - TRANSFAC, A database of transcription factors and their binding sites:
TRANSFAC, Braunschweig, Germany
Suggest a tool or resource
- Please contact Flybase to suggest a tool or resource for the list.