Organism-specific databases

Last modified: June 14, 2005

Organisms

Eukaryotes

Caenorhabditis elegans

• Bionet.celegans Newsgroup Archive
• C. briggsae BLAST server
• C. elegans BLAST server
• C. elegans interactome - Protein-Protein Interaction Maps
• C. elegans gene knockout consortium
• C. elegans genes in KEGG
• C. elegans WWW server (US homepage) Greek mirror
• Ensembl C. briggsae genome server
• Ensembl C. elegans genome server
• Fire lab vectors
• Get Worm DNA
• NEXTDB- The NEmatode EXpression DataBase
• TIGR C. elegans gene index
• TIGR C. elegans gene ontology
• Intronerator - Tool to explore introns and alternative splicing in C. elegans
• RNAi Database
• WILMA - automated protein annotation, including C. elegans
• WORFDB - Worm Open Reading Frame Database
• WORMBASE - Comprehensive Worm Genome Database
• Wormpep
• Worm Atlas - C. elegans anatomy
• Links to other nematode sites
• Worms on the Web - Links to other nematode sites
• OnchoNet Links - Links to other parasitic nematode sites

Mouse

Mouse genomic databases

• Ensembl mouse genome server
• Mouse Genome Informatics
• Genetic and physical maps of the Mouse Genome
• The Mouse Genome Project
• Mouse Genome Resources - (NCBI)
• Mouse imprinted genes
• Dysmorphic Human-Mouse Homology Database
• Portable dictionary of the mouse genome
• Whole mouse catalog - jumpsite

  Transgenic and Knockout mouse mutants

• Cre transgenic database
• EMMA European Mouse Mutant Archive
• German Mouse Clinic Mouse phenotyping center with open access to the scientific community
• Mouse knockout and mutation database
• Mouse knockout database
• Omnibank knockout clones - library of 200,000 mouse knockout stem cells for academic research
• ORNL Mutant Mouse Database
• Mouse models of human cancer
• Mouse models of human disease

  Mouse mutants generated by Gene Trap Insertion

• BayGenomics Gene Trap Database
• EMMA European Mouse Mutant Archive
• Manitoba Gene Trap Database
• Soriano Gene Trap Lines

  Mouse mutants generated by ENU Mutagenesis

• Baylor College of Medicine: Mouse Mutagenesis for Development Defects
• EMMA European Mouse Mutant Archive
• GSF: The ENU-Mouse Mutagenesis Screen Project
• Harwell Mutagenesis Programme
• The Jackson Laboratory Neurological Mouse Mutants
• The Jackson Laboratory: Mouse Mutants with Heart, Lung, Blood and Sleep Disorders
• Oak Ridge National Laboratory: Mammalian Genetics and Genomics
• Tennessee Mouse Genome Consortium
• McLaughlin Research Institute
• RIKEN Genomic Sciences Center: Large-Scale Mutagenesis Project

  Mouse anatomy and pathology

• The Anatomy of the Laboratory Mouse (1965) by Margaret J. Cook, adapted for the Web by MGI
• The Caltech µMRI Atlas of Mouse Development
• Edinburgh Mouse Atlas- 3-D embryo anatomy
• Pathology of Genetically Engineered Mice
• Necropsy of the Mouse - Detailed, well-illustrated introduction
• The Mouse Brain Library
• Mouse Tumor Biology Database
• Pathbase
• The Virtual Mouse NecropsyMouse Pathology
• The Visible MouseMouse Anatomy, Physiology, Histology and Pathology

Rat

• Curamap Rat Radiation Hybrid Map
• Ensembl rat genome server
• Rat Genome Database
• Rat Genome Resources - (NCBI)
• Guides for organ sampling and trimming procedures in rats

Fly

• Berkeley Drosophila genome project
• Drosophila genome overview - (NCBI)
• Drosophila genes in KEGG
• Ensembl fruitfly genome server
• Flybase - (Indiana University)
• FlyBrain
• Flyserver - access to FlyView image database and FlyMove multimedia database
• The Interactive Fly - Comprehensive Fly Database
• TIGR Drosophila Gene Index
• World-Wibe Web Virtual Library: Drosophila

Fish

Fugu

• Ensembl Fugu genome server
• Fugu Genome Analysis - (HGMP)

Tetraodon nigroviridis

• Tetraodon nigroviridis Database - (Whitehead Institute)

Zebrafish

• Ensembl Zebrafish genome server
• Zebrafish Genome Resources - (NCBI)

Farm animals

• ArkDB farm animal database (cat, chicken, cow, deer, horse, pig, salmon, sheep, tilapia, turkey)

Other animals

• Ciona savignyi Database - (Whitehead Institute)

Parasites

• TIGR Theileria parva database
• TIGR Parasites database
• OnchoNet Links - Links to parasitic nematode sites

Fungi

Yeast

• Saccharomyces Genome Database
• Comprehensive Yeast Genome Database
• Pathcalling Yeast Interaction Database
• TRIPLES TRansposon Insertion Phenotypes, Localization, and Expression in Saccharomyces
• S. pombe Genome Sequencing Project

Other Fungi

• Magnaporthe grisea Database - (Whitehead Institute)
• Neurospora crassa Genome Database - (Whitehead Institute)
• TIGR Fungal database

Plants

Arabidopsis thaliana

• MIPS Arabidopsis thaliana database
• The Arabidopsis information resource
• TIGR Arabidopsis thaliana database

Rice

• Rice Genome Database
• TIGR Rice Genome Project

Prokaryotes

Escherichia coli

• Ecocyc - Encyclopedia of Escherichia coli K12 Genes and Metabolism
• Ecogene
• RegulonDB- Database on Transcriptional Regulation and Genome Organization

Microbial Genomes

• Comprehensive Microbial Resource
• Microbial Genome Database for Comparative Analysis
• TIGR Microbial Database

If you have any comments or suggestions be sure to let me know!

Peter Taschner  -  P.Taschner@lumc.nl