Tools for gene prediction
Sofberry (gene finding)
Sofberry(gene finding with similarity)

Tools for gene expression
PLEXdb (Plant Expression Database)
ExpressWeb (Expression db Website)

Tools for promoter analysis
PLACE (Plant Cis-acting Regulatory DNA Elements)
PlantCARE (Cis-Acting Regulatory Element)
PlantPAN 3.0 (Plant Promoter Analysis Navigator)
Promoter 2.0 Prediction Server
Softberry (Recognition of PLANT Regulatory motifs conserved )

Tools for alignment and phylogeny

General databases
UniProt Knowledgebase (Swiss-Prot + TrEMBL)
TGI, The Gene Index Project (EST database + compilation)
GeneDB (genome database)
NCBI (genome and EST database)
JGI (genome and EST database)
SUPERFAMILY (genome database)

Unicellular algae
Protist databases
Prokaryote databases
CyanoBase (Cyanobacteria genome database)
J. Craig Venter Institute (genome database)