General

National Center for Biotechnology Information (NCBI)
European Bioinformatics Institute (EBI)
DNA Data Bank of Japan (DDBJ)
The Institute for Genomics Research (TIGR)
GenomeWeb
BioMedNet
Virtual Library Biosciences
Clemson University Genomics Institute (CUGI)

University of Missouri (MU)

MU Center for Sustainable Energy

Bradyrhizobium japonicum

Bradyrhizobium genome

Soybean 

Soybean Knowledge Base (SoyKB)
Legume Genomics Website
United Soybean Board (USB)
Soybean Genomics Consortium
Soybase
Soybean Physical Map
Soybean Genomics and Biotechnology Center
North Central Soybean Research Program (NCSRP)
Missouri Soybean Merchandising Council (MSMC)
TIGR Soybean Gene Index (TIGR)

Arabidopsis

The Arabidopsis Information Resource (TAIR)
Arabidopsis Functional Genomics Consortium (AFGC)
Salk Institute Genomic Analysis Laboratory (SIGnAL)
The Sainsbury Laboratory
Syngenta Arabidopsis Insertion Library (SAIL)

Model Legumes

Medicago truncatula Consortium
TIGR Medicago truncatula Gene Index (TIGR)
Center for Medicago Genomics Research (Noble Foundation)
Medicago whole genome sequencing (Univ. of Oklahoma)
European Projects on Medicago truncatula
Lotus japonicus EST and genome sequencing (Kazusa DNA Research Institute)

Gene Identification

Computational Biology at ORNL
GENESCAN

Protein

Pfam
Protein Information Resource (PIR)
Protein Data Bank (PDB)
InterPro

Biochemical Pathways

Kyoto Encyclopedia of Genes and Genomes (KEGG)
The pathway resource list

Protocols

Molecular Biology Protocols
Cell and Molecular Biology Protocols

Others

SAGE Home Page
Biology WorkBench