Databases

Select on of the headings below...

Genetic and Physical Mapping
Specialized Genomics
Sequence
Germplasm 
Arabidopis
Rice
Fungi

Genetic and Physical Mapping Databases

by species:
AtDB (TAIR) (Arabidopsis thaliana: thale cress) more Arabidopsis databases
BeanGenes  (Phaseolus, Vigna spp.: common bean, tepary bean, cowpea, mungbean etc.)
BrassicaDB (Brassica napus: rape)
GrainGenes (Triticum and Aegilops spp. and Saccharum : wheat, barley, oats, rye, and sugarcane)
MaizeDB  (Zea maize: corn)
Rice Genome Research Program (Oryza sativa: rice)
SolGenes (Lycopersicon, Solanum etc.: tomato, potato etc.)
Soybase  (Glycine max: soybean)

TIGR databases
The Institute for Genomic Research Databases (TIGR)
   Thale Cress (Arabidopisis thaliana)
   Rice (Oryza sativa)
   Potato (Solanum tuberosum)

link lists:
CMS list of plant databases
USDA list of plant databases
U.S. ARS Genome Database Resource (with links to the genome databases of many species, including the grasses)
BAC centre at Texas A&M (BAC libraries for most of the important plant species)
NRC - Canadian Bioinformatics Resource (Database access tools)
Japan - Database of Research Tools
Japan - GenomeNet
Japan - Genomics Databases

Sequence Databases

Genbank at The National Center for Biotechnology Information (NCBI)
     sequence databases
       dbEST(expressed sequence tags)
       dbGSS(genome survey sequences)
       dbSTS(sequence tagged sites)
       dbSNP(single nucleotide polymorphisms)

     Entrez: NCBI's search and retrieval system
       structure(3-D macromolecular structures for proteins and polynucleotides)
       genome(the whole genomes of over 800 organisms)
       protein(protein entries from SwissProt, PIR, PRF, PDB, and translations from coding regions in GenBank and RefSeq)
       nucleotide(nucleotide entries from GenBank)
       Pubmed(the biomedical literature)
       taxonomy(contains the names of all organisms that are represented in the genetic databases)

EMBL and DDBJ, the other two major international sequence databases exchange sequence with Genbank on a daily basis.

EMBL European Molecular Biology Laboratory (Europe's primary nucleotide sequence resource)
DDBJ DNA Data Bank of Japan (The sole DNA data bank in Japan)
VectorDB(Molecular Biology Vector Sequence Database)

 
Germplasm Databases/Repositories

The Germplasm Resources Information Network (GRIN)
    National Plant Germplasm System (NPGS)
    GRIN's list of related sites

American Type Culture Collection (ATCC)
     Plant Viruses
     Plant Tissue Cultures
     Plant Seeds
     Fungi and Yeasts
     Bacteria
     Molecular Biology

Arabidopis Databases

Plant Plasma Membrane Database (PPMdb) A. thaliana plasma membrane proteins with expression and sequence data
AtDB (TAIR) genetic and physical mapping data
Arabidopsis thaliana Chromosome 4 - Genetic/Physical Maps at the BBSRC John Innes Centre 
Arabidopsis Information Management System (AIMS) stock ordering and information center for the ABRC 
Arabidopsis cDNA Sequence Analysis Project
The Arabidopsis Genome Center (ATGC)
"Everything Arabidopsis" Resource
The TIGR Arabidopsis Database Project

Rice

Rice Genome Database (Beijing Genomics Institute)
Rice Genome Project (Syngenta)

Miscellany

Transcription Regulatory Regions Database  transcription factor binding sites, promoters, enhancers, silencers, etc.
codon usage database a large list of organisms available
Transterm  messenger RNA components and signals 
The Signaling PAthway Database (SPAD)  genetic information and signal transduction systems
ChromDB  plant chromatin database.
PlantsP  functional genomics database of plant phosphorylation.
PLACE  database of plant cis-acting regulatory DNA elements.

Fungi

Fungal Genetics Stock Center
        Cloned genes and gene libraries Fungal Genetics Stock Center
INRA MycorWeb Ectomycorrhizas database