Revision as of 16:15, 3 October 2015

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
Electron micrograph maps of D. melanogaster polytene chromosomes:
Sorsa Maps, Helsinki, Finland
FlyBrain, an Online Atlas and Database of the Drosophila Nervous System:
FlyBrain, University of Arizona, Tucson, USA
FlyCircuit, a Database of Drosophila Brain Neurons:
FlyCircuit, National Tsing Hua University, Taiwan
FlyGut, An interactive Database that aims to provide a comprehensive atlas of the Drosophila melanogaster adult midgut (see also, FlyGut-seq):
Buchon Lab, Cornell University, Ithaca, NY, USA & Lemaitre Lab, EPFL, Lausanne, Switzerland
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 describing marker phenotypes in the fruit fly:
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
Scans of Bridges' original 1935 polytene drawings for D. melanogaster:
GEM Website, University of Hawaii, 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

Cas9 Design:
Center for Bioinformatics, Peking University, Peking, China
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, Harvard Medical School, Boston, MA, USA
DRSC Finding CRISPRs, Drosophila CRISPR gRNA design search tool:
DRSC, 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
TAL Effectors:
Zhang lab, MIT, 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
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

Data and Metadata for Drosophila Genomes

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. ananassae Genome:
D. ananassae Organism Overview, NCBI, USA
D. ananassae Genome Assembly Report, NCBI, USA
D. ananassae 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. 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. 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. 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
cisPatterns, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:
Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA
DGRC, Cell Line Expression tool (based on modENCODE data):
DGRC, University of Indiana, Bloomington, IN, USA
DRSC, Cell Line Expression tool (based on modENCODE data):
DRSC, Harvard Medical School, Boston, MA, USA
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
GEO Profiles, Gene Expression Omnibus:
GEO, NCBI, Bethesda, MD USA
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, Reports on functionally related genes:
Gene group list, FlyBase, Bloomington, IN and Cambridge, MA, USA, Cambridge, UK
GLAD, an Online Database of Gene List Annotations for Drosophila:
DRSC, 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
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, 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, 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
SignaLink, A signaling pathway resource with multi-layered regulatory networks:
SignaLink, Eötvös Loránd University of Science, Budapest, Hungary
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
PhenomicDB, A Cross-species Genotype-Phenotype Resource:
Phenotype-Genotype Database, Berlin, Germany
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

ncRNA Databases and Tools

DIANA microT-CDS, MicroRNA Target Prediction:
DIANA microT-CDS, DIANA LAB, Athens, Greece
DIANA TarBase, MicroRNA Target Database:
DIANA TarBase, DIANA LAB, Athens, Greece
GtRNAdb, tRNAscan-SE analysis of complete genomes:
GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA
MinoTar, Predict microRNA Targets in Coding Sequence:
MinoTar, DRSC, Harvard Medical School, Boston, MA, USA
miRBase, microRNA data:
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.

miRNA, Target Gene Prediction:
miRNA - Target Prediction, EMBL, Heidelberg, Germany
miRNA_Targets:
miRNA targets on full length mRNAs, Deakin University, Victoria, Australia
miRTarBase, Experimentally Validated microRNA-target Interactions Database:
miRTarBase, ISBLab, Hsinchu, Taiwan
Rfam, RNA families database of alignments and CMs:
Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA
RNAcentral, provides unified access to the ncRNA sequence data supplied by multiple Expert Databases:
RNAcentral, EMBL-EBI, Hingston, UK
snOPY, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:
snOPY, University of Miyazaki, Japan
TargetScanFly, Prediction of microRNA targets:
TargetScanFly, Whitehead Institute and MIT Dept. of Biology, 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, Harvard Medical School, Boston, MA, USA
DIOPT-DIST: DIOPT Diseases and Traits, DRSC Disease Gene Query Tool:
DRSC, 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
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

Assembly/Alignment/Annotation of 12 related Drosophila species:
Assembly/Alignment/Annotation, LBNL, USA
DIOPT, DRSC Integrative Ortholog Prediction Tool:
DRSC, 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, UniversitÃ© Libre de Bruxelles, Belgium
OrthoDB, the Hierarchical Catalog of Orthologs:
http://orthodb.org/orthodb7 OrthoDB, University of Geneva, Switzerland]
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 Polymorphism Database:
DGRP2, Univ. AutÃ²noma de 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

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
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
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
Genetic Portraits, An overview of commonly used model organisms in genetic research:
McGraw-Hill Higher Education
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, Drosophila RNAi Screening Center:
DRSC, Harvard Medical School, Boston, MA, USA
Search by gene(s) to find hits in DRSC screens:
DRSC, 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, 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, Harvard Medical School, Boston, MA, USA
Predicted Off-Target Free Sequence Regions:
DRSC, 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, Harvard Medical School, Boston, MA, USA
SnapDragon, RNAi Design:
DRSC, Harvard Medical School, Boston, MA, USA
TRiP, Transgenic RNAi Project:
Transgenic RNAi Project, DRSC, 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, 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
cis-analyst, Searching the Drosophila genome for clusters of binding sites:
cis-analyst, 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
FlyReg, DNase I Footprint Database:
University of Manchester Bioinformatics Resources, University of Manchester, UK
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
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
PREdictor, to identify Polycomb/Trithorax response elements:
PREdictor, Bielefeld University, Germany
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.

@@ Line 21: / Line 21: @@
 =CRISPRs and TALENs=
 * <b>Cas9 Design</b>:<br />[http://cas9.cbi.pku.edu.cn/ Center for Bioinformatics, Peking University, Peking, China]
-* <b>CCTop</b> CRISPR/Cas9 target online predictor:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
+* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
-* <b>CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.rc.fas.harvard.edu/about.php/ Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
-* <b>CRISPR Genome Engineering Resources</b>:<br />[http://www.genome-engineering.org/crispr/ Zhang lab, MIT, Boston, MA, USA]
+* <b>CRISPOR</b> Model organism gRNA design tool:<br />[http://tefor.net/crispor/crispor.cgi/ TEFOR, Gif-sur-Yvette, France]
+* <b>CRISPR/Cas Web Resources</b> Web Resources for design and planning of CRISPR/Cas9 studies:<br />[http://igtrcn.org/knowledgebase/crisprcas-web-resources// IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA]
+* <b>CRISPR-ERA</b> A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:<br />[http://crispr-era.stanford.edu// Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA]
+* <b>CRISPR Genome Engineering Resources</b> CRISPR Design Tool:<br />[http://www.genome-engineering.org/crispr/?page_id=41/  Zhang Lab, MIT, Boston, MA, USA]
 * <b>CRISPR fly design</b> -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://www.crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
+* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
+* <b>DRSC CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>DRSC Finding CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC, Harvard Medical School, Boston, MA, USA]
 * <b>E-CRISP</b>, Design of CRISPR Constructs:<br />[http://www.e-crisp.org/E-CRISP/designcrispr.html DKFZ/Boutros lab, Heildelberg, Germany]
 * <b>E-TALEN</b>, Design of TALEN Constructs:<br />[http://www.e-talen.org/E-TALEN/ DKFZ/Boutros lab, Heildelberg, Germany]
-* <b>Finding CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC, Harvard Medical School, Boston, MA, USA]
 * <b>flyCRISPR</b>, Resource Site: <br />[http://flycrispr.molbio.wisc.edu/ O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA]
 * <b>flyCRISPR</b>, Optimal Target Finder:<br />[http://tools.flycrispr.molbio.wisc.edu/targetFinder/ O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA]
@@ Line 84: / Line 89: @@
 * <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
 * <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
+* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[http://bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
 * <b><em>cis</em>Patterns</b>, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:<br />[http://cispatterns.ninds.nih.gov/ Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA]
 * <b>DGRC, Cell Line Expression tool</b> (based on modENCODE data):<br />[https://dgrc.cgb.indiana.edu/cells/TilingSearch DGRC, University of Indiana, Bloomington, IN, USA]
@@ Line 94: / Line 100: @@
 * <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
 * <b>FlyLight</b>, Expression Patterns of GAL4 Driver Lines:<br />[http://flweb.janelia.org/cgi-bin/flew.cgi HHMI, Janelia Farms Research Campus]
+* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 * <b>flytrap</b>, a database of P{GAL4} enhancer traps and their expression in brains: <br />[http://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
 * <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
@@ Line 99: / Line 106: @@
 =Gene Groups=
-* <b>FlyBase Gene Group Reports</b>:<br />[http://flybase.org/static_pages/feature/previous/articles/2015_05/gene_groups.html FlyBase Consortium]
+* <b>FlyBase Gene Groups</b>, Reports on functionally related genes:<br /> [http://flybase.org/static_pages/FBgg/browse.html Gene group list, FlyBase, Bloomington, IN and Cambridge, MA, USA, Cambridge, UK]
 * <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [http://www.flyrnai.org/tools/glad/web/ DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [http://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+* <b>Interactive fly</b>, Maternally transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/4matrnl.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+* <b>Interactive fly</b>, Zygotically transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/5zygotic.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+* <b>KEGG BRITE</b>, Functional hierarchies and binary relationships of biological entities:<br /> [http://www.genome.jp/kegg/brite.html KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan]
+* <b>UCSC D. melanogaster Gene Sorter</b>, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:<br /> [https://genome.ucsc.edu/cgi-bin/hgNear?org=D.+melanogaster UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA]
 =General Bioinformatics Tools=
@@ Line 106: / Line 118: @@
 * <b>BioMart</b>, Data Warehouse:<br />[http://www.biomart.org/ BioMart, EMBL-EBI, OICR, SRSI]
 * <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[http://www.cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
-* <b>DAVID (NIH)</b> -- Database for Annotation , Visualization and Integrated Discovery:<br />[http://david.abcc.ncifcrf.gov/ DAVID, NIH, Bethesda, MD, USA]
 * <b>DNA & Protein Work List</b>, A list of tools aggregated by the Prokop Lab:<br />[http://www.prokop.co.uk/Links/tools.html http://www.prokop.co.uk/Links/tools.html]
 * <b>FlyMine</b>, an Integrated Database for Drosophila and Anopheles Genomics:<br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
@@ Line 112: / Line 123: @@
 * <b>Galaxy</b>: Open Source Bioinformatics Tools:<br />[https://usegalaxy.org/ Galaxy, Penn State, PA USA and Emory University, GA USA]
 * <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[http://www.broadinstitute.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
-* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
 =Genome Sequencing Projects=
@@ Line 127: / Line 137: @@
 * <b>FlyNet Human Disease Prioritization</b>:<br /> [http://www.inetbio.org/flynet/Network_fly_comm.php NetBioLab, Yonsei University, Seoul, Korea]
 * <b>HuDis</b>, high confidence human disease gene - fly gene ortholog pairs:<br />[http://www.flyrnai.org/HuDis DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>MORPHIN</b>, Model ORganism Projected on a Human Integrated gene Network:<br />[http://www.inetbio.org/morphin/index.php MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA.]
+* <b>NeuroGeM</b>, A knowledgebase of genetic modifiers in neurodegenerative diseases:<br />[http://chibi.ubc.ca/neurogem/ CHiBi, The University of British Columbia, Vancouver, BC, Canada]
 =Interaction and Pathway Databases=
 * <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
 * <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>DAPPER</b>, database for protein-protein interactions:<br/>[http://dapper.gen.cam.ac.uk/ DAPPER, University of Cambridge, Cambridge, UK]
 * <b>DPiM</b>, Drosophila Protein interaction Map:<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
 * <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
@@ Line 136: / Line 149: @@
 * <b>FlyCyc</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 * <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
+* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 * <b>FlyReactome</b> -- a Curated Knowledgebase of Drosophila melanogaster Pathways:<br />[http://fly.reactome.org FlyReactome, University of Cambridge, Cambridge, UK]
 * <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
@@ Line 141: / Line 155: @@
 * <b>KEGG</b> -- Kyoto Encyclopedia of Genes and Genomes:<br />[http://www.genome.jp/kegg KEGG, Kyoto, Japan]
 * <b>Reactome Pathway Database</b>:<br />[http://www.reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
+* <b>SignaLink</b>, A signaling pathway resource with multi-layered regulatory networks:<br />[http://http://signalink.org/ SignaLink, Eötvös Loránd University of Science, Budapest, Hungary]
 * <b>SignedPPI</b>, Searchable Database of Known and Predicted Protein-protein Interactions:<br />[http://www.flyrnai.org/SignedPPI/ DRSC, Harvard Medical School, Boston, MA, USA]
 * <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
+* <b>WikiPathways</b>, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:<br />[http://www.wikipathways.org/index.php/WikiPathways WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands]
 =Laboratory Resources=
 * <b>Laboratory Manual of Drosophila</b>: <br />[http://darwin.bio.uci.edu/~mueller/pdf/Lab_manual.pdf PDF, Chippindale, A. ''et al''., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA]
-=miRNA and ncRNA Databases and Tools=
-* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/ DIANA microT-CDS, DIANA LAB, Athens, Greece]
-* <b>DIANA TarBase</b>, MicroRNA Target Database:<br />[http://diana.imis.athena-innovation.gr/DianaTools/ DIANA TarBase,, DIANA LAB, Athens, Greece]
-* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence:<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
-* <b>miRBase</b>, microRNA data:<br />[http://www.mirbase.org/ 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.
-* <b>miRNA, Target Gene Prediction</b>:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
-* <b>miRNA_Targets</b>:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
-* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
-* <b>Rfam</b>, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA]
-* <b>TargetScanFly</b>, Prediction of microRNA targets:<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA]]
 =Miscellaneous=
@@ Line 168: / Line 172: @@
 * <b>GenAge</b> -- The Ageing Gene Database:<br />[http://genomics.senescence.info/genes/ Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
 * <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>IGTRCN</b>, Insect Genetic Technologies Research Coordination Network:<br />[http://igtrcn.org// IGTRCN, University of Maryland, Rockville, MD, USA]
 * <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
 * <b>Jfly</b>, a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:<br />[http://jfly.iam.u-tokyo.ac.jp/ Jfly, University of Tokyo, Japan]
@@ Line 178: / Line 183: @@
 * <b>What's hot today:</b> Current papers in developmental biology and gene function:<br />[http://www.sdbonline.org/sites/fly/aimain/model-organisms-this-week.htm Interactive Fly, Bethesda, MD, USA]
 * <b>The WWW Virtual Library--Drosophila</b>:<br />[http://www.ceolas.org/fly/ Drosophila Virtual Library]
+=ncRNA Databases and Tools=
+* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
+* <b>DIANA TarBase</b>, MicroRNA Target Database:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index DIANA TarBase, DIANA LAB, Athens, Greece]
+* <b>GtRNAdb</b>, tRNAscan-SE analysis of complete genomes:<br />[http://gtrnadb.ucsc.edu/ GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA]
+* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence:<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>miRBase</b>, microRNA data:<br />[http://www.mirbase.org/ 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.
+* <b>miRNA, Target Gene Prediction</b>:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
+* <b>miRNA_Targets</b>:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
+* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
+* <b>Rfam</b>, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA]
+* <b>RNAcentral</b>, provides unified access to the ncRNA sequence data supplied by multiple Expert Databases:<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hingston, UK]
+* <b>snOPY</b>, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:<br />[http://snoopy.med.miyazaki-u.ac.jp/ snOPY, University of Miyazaki, Japan ]
+* <b>TargetScanFly</b>, Prediction of microRNA targets:<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA]]
+=Ontology Resources=
+* <b>AmiGO 2</b>, tools for searching and browsing the Gene Ontology database:<br />[http://amigo2.berkeleybop.org/amigo AmiGO 2, Berkeley Bioinformatics Open-source Projects, USA]
+* <b>BioPortal</b>, a biomedical ontologies repository and browser:<br />[http://bioportal.bioontology.org/ BioPortal, The National Center for Biomedical Ontology, USA]
+* <b>Disease Ontology</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
+* <b>Gene Ontology Consortium</b><br />[http://geneontology.org/ Gene Ontology Consortium]
+* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
+* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
+* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.github.io/ OboFoundry]
+* <b>Ontobee</b>, an ontologies browser:<br />[http://www.ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
+* <b>Ontology Lookup Service</b>, an ontologies browser:<br />[http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
+* <b>Protege</b>, browser for OWL ontologies:<br />[http://protege.stanford.edu/products.php, Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA]
+* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[http://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
+=Orthology Predictions=
+* <b>Compara</b>, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.<br />[http://useast.ensembl.org/info/genome/compara/index.html?redirect=no Ensembl, Hinxton, UK]
+* <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool<br />[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>DIOPT-DIST: DIOPT Diseases and Traits</b>, DRSC Disease Gene Query Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/#/app/home Computational Biology Group, EMBL, Heidelberg, Germany]
+* <b>Homologene</b>, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MD, USA]
+* <b>Inparanoid</b>, InParanoid: ortholog groups with inparalogs<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Stockholm Bioinformatics Centre, Stockholm, Sweden]
+* <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://groups.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA]
+* <b>OMA Browser</b>, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.<br />[http://omabrowser.org/oma/home/ Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158]
+* <b>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[http://orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
+* <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[http://www.orthomcl.org/orthomcl/ EuPathDB]
+* <b>PhylomeDB</b>, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)<br />[http://phylomedb.org/ Comparative Genomics Groups at CRB, Barcelona, Spain]
+* <b>Roundup</b>, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.<br />[http://wall-lab.stanford.edu/projects/roundup/ Wall lab, Stanford University, Palo Alto, CA, USA]
+* <b>TreeFam</b>, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.<br />[http://www.treefam.org/ EMBL-EBI, Hinxton, UK]
 =Phylogenetic Comparison Tools=
@@ Line 183: / Line 231: @@
 * <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC, Harvard Medical School, Boston, MA, USA]
 * <b>EvoPrinter</b>, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
+* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
 * <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
 * <b>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, UniversitÃ© Libre de Bruxelles, Belgium]
-* <b>NCBI HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
 * <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />http://orthodb.org/orthodb7 OrthoDB, University of Geneva, Switzerland]
 * <b>Vista Tools</b> -- Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome:<br />[http://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA]
@@ Line 202: / Line 250: @@
 * <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[http://expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
 * <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
-* <b>InterPro protein domain analysis of Drosophila</b>:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
+* <b>InterPro</b> protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
 * <b>MEROPS</b>, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
-* <b>Panther protein classification system</b>:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
+* <b>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
 * <b>PDB</b>, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 * <b>PhospoPep</b>, interactive interrogation of MS-derived phosphorylation data from 4 different organisms: <br />[http://www.phosphopep.org/index.php Institute for Systems Biology, Seattle, Washington, USA]
@@ Line 265: / Line 313: @@
 * <b>EPD</b>, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland]
 * <b>Fly Factor Survey</b> - Database of Drosophila TF DNA-binding Specificitiies: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA]
+* <b>i-cisTarget</b>, An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly:<br />[http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/ i-cisTarget, University of Leuven, Leuven, Belgium]
+* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 * <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, USA]
-* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 * <b>PREdictor</b>, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany]
 * <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]

Difference between revisions of "FlyBase:Drosophila Online Resources"