Links to other on-line resources

Principle sources of Drosophila information

The World-Wide Web Virtual Library: Drosophila
FlyBase - Indiana University
Berkeley Drosophila Genome Project
Patterns of gene expression in Drosophila embryogenesis - From the BDGP
TIGR Drosophila Gene Index
FlyView
Flybrain
Drosophila melanogaster genes: KEGG metabolic and regulatory pathways
Drosophila at NCBI
Drosophila Segmentation Genes Nets
FlyMove:
Jfly Web for Drosophila Researchers
Drosophila Information Service

Insect resources

Iowa State - Entomology Index
Colorado State University - Entomology Resources
Medical research council - Insect Genome Databases Menu
Illinois State Acadamy of Science - Entomology Links
Department of Entomology U.C. Riverside - Insects on the Internet
Insects on WWW - Maintained by Jun Fan of Virginia Tech
Entomology Department - American Museum of Natural History
Featured Creatures - University of Florida's Department of Entomology and Nematology

Developmental biology resources

The Society for Developmental Biology
The Virtual Library - Developmental Biology
The Developmental Biology Cinema
The Virtual Embryo
Zygote: a website for information on Developmental Biology
Sive Lab - General Developmental Biology Links

Drosophila laboratories, computational sites and sources of stocks

Gerard Mannings List of Drosophila Research Labs on the Web
Bioscience and Fly Links - Kendel Broadie
Sean Carroll's Lab - University of Wisconsin
Rubin Lab Methods Book - Nicholas Baker lab, Albert Einstein University
GenePalette - A desktop application for genome sequence visualization and navigation - Posakony lab, UCSD
The Drosophila melanogaster Malpighian tubule
The Drosophila Microarray Project
Homophila: Human Disease to Drosophila Gene Database
Fly Enhancer: Search the Drosophila genome for clusters of transcription factor binding sites
Hyper-Neuroblast Map - Chris Doe's Lab
Synapse formation in Drosophila - Andreas Prokof's Lab
Bloomington Drosophila Stock Center - at Indiana University
Developmental Studies Hybridoma Bank - at the University of Iowa
FlyTrap - GFP protein trap database - Lynn Cooley's lab
Fly Trap - A database of P{Gal4} enhancer traps and their expression in brains
P-Screen - P-element Screen / Gene disruption project of the Bellen/Rubin/Spradling labs
Andrea Brand laboratory - Includes images and movies of CNS development
Motor Axon guidance primer - Zinn lab
P Elements in Drosophila - Engels lab
Robert T. Simpson Laboratory at Penn State
Drosophila visual receptors - Stark lab
Microbial infection of Drosophila : a model for dissecting host-pathogen interactions - Bruno Lemaitre's lab

Genome and bioinformatics links

• General Sites
  PubMed/Medline Query - National Library of Medicine
       As of 2004 this resource includes over 14 million citations for biomedical articles back to the 1950's.
  SRS - European Bioinformatics Institute
       A powerful data integration platform providing rapid access to life science data stored in more than 400 databases.
       Use this resource to recover almost any information, including structure, evolution and literature about any gene
       or protein of interest.
  Biocarta: Observe how genes interact
       Dynamic graphical models of gene interaction
  GenMAPP: UCSF
       Human, mouse, yeast and rat gene expression datasets visualized using the GenMAPP application program
  American Association for Laboratory Animal Science
       The "Links" page consists of the following subcategories: Associations, comparative medicine departments,
       diagnostic labs and testing alternatives. See for example University of California Center for Animal Alternatives
        and The Animal Welfare Information Center of U.S. Department of Agriculture
• Multiple Resource Sites
  Database resources of NCBI
       Major databases include PubMed, nucleotide and protein sequences, protein structures, complete genomes and taxonomy.
  ExPASy Molecular Biology Server - proteomics server of the Swiss Institute of Bioinformatics
       Databases include Swiss-Prot and TrEMBL, PROSITE, SWISS-2DPAGE and SWISS-3DIMAGE.
  Database Resources of the Sanger Institute
       Database resources include (1) Pfam, a protein families database, (2) Rfam, an RNA families database of alignments,
        (3) Wormbase, a C. elegans genome database browser, and (4) SRS, a sequence retrieval system.
  Ensembl Genome Browser - Sanger Center
       BLAST server and sequence retrieval for several species, including human, chimp, mouse, rat, zebrafish, fugu, mosquito,
       fruitfly, C. elegans and C. Briggsae
  CMS Molecular Biology Resource - San Diego Supercomputer Center at UCSD
       A compendium of tools and resources for molecular biology
• Molecular Analysis Sites
  LocusLink - National Library of Medicine
       LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.
       It presents information on official nomenclature, sequence accessions, phenotypes, precomputed blast,
       and includes links to UniGene clusters with further links to the HomoloGene resource, which contains literature links.
  Entrez Protein - National Library of Medicine
       Along with Entrez Nucleotide, a redundant database of sequences providing citations and other relevant links
  SwissProt - Swiss Institute of Bioinformatics
       A curated protein sequence database, which strives to provide a high level of annotation (such as the description of the
        function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level
       of redundancy and high level of integration with other database.
  iProClass - Georgetown University
       An integrated resource that provides comprehensive family relationships and structural/functional features of proteins.
       Consists of non-redundant Protein Information Resource (PIR) and SwissProt/TrEMBL proteins organized with more than
       36,290 PIR superfamilies, 145,300 families, 7255 domains, 1300 motifs, 280 post-translational modification sites,
       and links to over 50 biological databases.
  NCBI BLAST server
       Tools for recovery of protein and nucleic acid alignments
  Pfam: A Collection of Protein Domain Families - Sanger Institute
       A collection of multiple sequence alignments and hidden Markov models covering many common protein domains
       and families

• Human Bioinformatics Sites
  UCSC Genome Bioinformatics - Genome Bioinformatics Group of UC Santa Cruz
       Human Genome and Human Gene Family Browsers
  Online Mendelian Inheritance in Man - NCBI
       Catalog of human genes and genetic disorders
  GeneCards - Weizmann Institute of Science
       A database of human genes, their products and their involvement in diseases
  Harvester - EMBL Heidelberg
       Harvester caches and cross-links public bioinformatic databases and prediction servers to provide fast access
       to protein specific bioinformatic information. Contains information on human proteins only
  OMIM Locus-specific mutation database links - NCBI
       Links to two dozen human genetic disease databases
  Variation Databases and Related Sites - complied by the Human Genome Variation Society
       Includes locus specific mutation databases, disease centered mutation databases, and central mutation & snp databases
  GeneDis - Tel Aviv University
       Human Genetic Disease Database - Describes mutations in a dozen human genetic diseases
  MEDLINEplus Health Information: Brain and Nervous System Topics - National Library of Medicine, NIH
       Links to dozens of sites related to human neural diseases
  The Alzheimer Disease Mutation Database - Human Genome Variation Society
       All reported mutations related to Alzheimer Disease. Mutations can be retrieved based on the gene, phenotype
       and publication.
  Links pertaining to Nervous System Diseases - Karolinska Institute Library
       Links to dozens of sites related to nervous system diseases

Gene family and gene specific sites

ATPases Associated with diverse cellular Activities (AAA) server
The World Wide Web Wnt Window
Chromatin Structure & Function
Cytokines Online Pathfinder Encyclopaedia
Eph receptors and their ligands
Myosin Home Page
Nucleosome and chromatin pages of Dmitry Pruss
Web links to Pc-G and trx-G material
The Protein Kinase Resource
Transcription factor classification from The Transcription Factor Database
GRAP Mutant Database - A database of mutant alleles of G-protein coupled receptors - University of Tromso, Norway

Model Organsims

• Caenorhabditis elegans
  • WormBase
         Accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans     and some related nematodes
  • WormBase: Neuron Search
         Displays the anatomy of each C. elegans neuron, its pedigree, and genes expressed in the lineage

• Zebrafish
  • ZFIN - Zebrafish Information Network - University of Oregon
         Search for wild-type stocks, mutant/transgenic lines, genes/markers clones or gene expression

• Xenopus
  • The Xenopus Molecular Marker Resource - University of Calgary
         Includes a BLAST tool, gene expression patterns, and compilation of literature
  • Axeldb - Deutsches Krebsforschungszentrum, Heidelberg
         A database focusing on gene expression in the frog

• Mice
  • Mouse Genome Informatics - The Jackson Laboratory
              Integrated access to data on the genetics, genomics, and biology of the laboratory mouse (UL)
  • Gene Ontology Browser - The Jackson Laboratory
    • Links to molecular function including cell adhesion molecule activity, motor activity. signal transducer activity, transcription regulator activity, and
    • Links to biological process including behavior, cellular process, and development
    • Links to cellular component including extracellular, cell projection, cell surface, cytoplasm and nucleus
  • Gene Family Information - The Jackson Laboratory
         Includes Adenylate cyclase, Calcium Channel and Synaptotagmin families
  • Gene Expression Data - The Jackson Laboratory
         Search by gene symbol, gene ontology classification, chromosomal location, developmental stage
         and anatomical structure
  • Mouse gene trapping in embryonic stem cells - BayGenomics of the University of California
          ES cell lines for the purpose of producing knockout mouse

• Pufferfish
  • Fugu BlastView - Sanger Institute
         The current Fugu data is unassembled. The compact nature of the genome is largely due
         to scarcity of dispersed repetitive sequences (<10%). Fugu has been proposed as a model vertebrate genome
         to understand the more complex human genome and other vertebrate genomes.

• Sea Squirt
  • Ciona intestinalis - At the DOE Joint Genome Institute
         Included is a Ciona BLAST server - The Ciona intestinalis genome is the smallest of any experimentally
         manipulable chordate. This organism provides a good system for exploring the evolutionary origins
         of the chordate lineage, from which all vertebrates evolved.

• Drosophila pseudoobscura
  • Drosophila pseudoobscura BLAST Server - Baylor College of medicine
         Analysis of homologies between D. melanogaster and D. pseudoobscura reveals high conservation
         in gene regulatory regions

• Honey Bee
  • Honey Bee Brain EST Project - The W. M. Keck Center for Comparative and Functional Genomics at University of Illinois at Urbana-Champaign
         Brain library ESTs were assigned molecular function and biological process using the Gene Ontology classification system. The site includes a BLAST tool.