Plant Genomes
Plant Genome Database, PlantGDB
Ortholog Search
Rice
Rice miRNA Knowledge Database
Cereal small RNA database (US-Davis)
Rice MPSS
TIGR Rice Genome Project (annotation, Tos17/ACdS/TDNA, Repeats, Syntenic Mapping, genetic/physical/sequencing maps, orthologs, domains/motifs) 
To fetch a segment of rice DNA from any of 12 chromosomes 
Batch_download TIGR rice gene features (such as protein sequences etc.)
TIGR Oryza Repeat DB (Oryza repeats) 
TIGR Plant Repeat DB (16 plant family and genera repeat DBs) 
TIGR Rice Gene Index 
To do Blast search against Rice genomes only (DNA, proteins etc)
NSF Rice Oligo Array (publicly available 70mer array and expression DB) 
Rice Codon Usage Table
Rice Genome Program (Japan) (sequence, markers, INE, IRGSP facts/news) 
Gramene (integrated grass comparative DB) 
IRRI (rice genetic resources) 
Oryzabase (Japan rice stock center, linkage map, sequence, etc; TAIR equivalent)  
KOME (rice FLcDNA clones) 
Rice Annotation DB (RGP Annotation DB)
INE (RGP viewer) 
Kasalth BAC ends BLAST server 
Worlwide Genetic Resources Link Page 
Rice Expression DB (Japan cDNA microarray site) 
Rice Tos17 Insertion DB 
Rice Proteome DB 
BGI Rice Genome Sequencing 
International Rice Functional Genomics Consortium 
G. Ahn tDNA Insertion Mutants 

Arabidopsis

To retrieve or fetch sequences from a region or multiple regions on the AGI Arabidopsis genome, developed by SIGnAL
To view the expression patterns of a given gene, use eFP, AtGenExpress Visualization Tool (AVT), or Genevestigator (Digital Northern, Gene Atlas, and Response Viewer)
Other useful tools: AtGDB View, MPSS, NASCArrays Digital Northern, NASCArrays Spot History, AtGenExpress Visualization Tool, MIPS View, NCBI-Entrez Gene. InParanoid Ortholog Groups,  T-DNA Express
If interested in analyzing one gene using all tools at once (eFP, AVT ... T-DNA express), use this TAIR's tool. Enter a locus number (for AtWRKY genes, check here), and then click "submit query". In the new window, click the locus name. A new window will popup; look for external links (middle portion of the window).
To display Arabidopsis SNP dataView the map of Arabidopsis genes (you can zoom in to 50 bp!)
 Primer DesignComparing two set of data
T-DNA related
All tools developed by  SIGnA
 Download Arabidopsis promoter, intron, coding region etc Draw maps of the Arabidopsis genome using a list of locus names (i.e. At1g01010) Searches databases and web sites to find information about a given Arabidopsis gene (even including publications for the gene of interest)
Download ALL Arabidopsis promoters, CDSs, introns, terminators etc.
Arabidopsis MPSS
LEHLE SEEDS Welcome & Home Page
AIMS Arabidopsis Information Management System
ABRC Home Page
Advanced PubMed Search
Arabidopsis lab at MRC-LMB Cambridge UK..
Arabidopsis Genome Analysis
LEHLE SEEDS Home Page
Arabidopsis Real time PCR protocol from TIGR, now The J. Craig Venter Institute
Stanford Genomic Resources
Sorghum
Sorghum Genome Database

Populus trichocarpa
Poplar Genome Annotation V1.1
NCBI Populus Genome
Transcription Factor Database (Peking Univesity)

Supplies_Instruments and Chemicals
Fisher Scientific - Life Science - New Lab Start-Up
Corning
Flasks_Kimble-Kontes
PCR Home - Applied Biosystems (PerkinElmer)
Omni International_ homogenizers, cell disrupters, tissue tearers, PCR kits, lab equipment, pol
Ultrasonic Homogenizer
L&R Manufacturing Company Home Page
Genomics
AFGC Website
Functional Genomics
Microarray Project
Genomic Solutions Inc. _ Specializing in microarray and proteomic robotics, software, and servi
Textco, Inc.
genome gateway > papers
Brown Lab Homepage
Molecular Biology Database List
eBioinformatics - Bioinformatics service provider including BioNavigator
Proteome, Inc
Useful Links in Plant Science
UK CropNet - The UK Crop Plant Bioinformatics Network
The Korea Rice Genome Database
Welcome to RiceGenes!
The Expressed Gene Anatomy Database (EGAD)
Genome Sequencing Center - GSC Home Page
TRANSFAC - The Transcription Factor Database
GOBASE - The Organelle Genome Database
ExPASy - SWISS-PROT and TrEMBL
PEDANT front page
Kyoto Encyclopedia of Genes and Genomes
MaizeDB -- Maize Genome Database
Transgenic and Targeted Mutation Research
Bioinformatics
Sequence Manipulation Suit (format conversion, sequence analysis, isoelectric point calculation etc)
Sequence Manipulation Suit 2 (Java scripts)
ExPASy (many useful tools such as translation, protein structure etc)
aBi (comprehensive collections of bioinformatics tools)
Nuclear Location Sequence prediction
LOCtree (works very well)
PRSORT (So so in accuracy)
Transmembrane Segment prediction
DAS (Dense Alignment Surface)
TMHMM2.0
EMBL-EBI
Evan Noynaert's Collection of Perl Resources
The Bioinformatics Resource - Web Site of the CCP11 project
Bioinformatics Links
Gerstein Group -- Yale Bioinformatics
UCLA Bioinformatics
BioInformatics at IMV
Bioinformatics Resources
SAfrica National Bioinformatics Institute
Pfam
Munich Information Centre for Protein Sequenc.
Softberry (commercial sources of all kinds of bioinformatic tools)
-- Transcription start site prediction (TSSP)

-- Alignment of 2 sequences
Blast 2
jaligner, need Java(TM) SE Runtime Environment and Java Web Start SIGnAL 
Blast Between Two Sequences

Journals
Australian Journal of Plant Physiology
BBA - Gene Structure and Expression
Biological Review of Cambridge
BioTechniques
Cell Press
Current Microbiology
EMBO-Journal
The FASEB Journal
Genes & Development
Journal of Biological Chemistry
Journal of Cell Biology
Journal of Experimental Botany
JMB Online
Molecular and Cellular Biology
Nature
New Phytologists
Photosynthetica
 Nucleic Acids Research
Physiologia Plantarum
Springer LINK_ Planta
Plant Breeding
Plant Cell
Plant, Cell & Environment
Plant and Cell Physiology
Plant Gene Reporter
Plant and Soil
Plant Journal
Plant Molecular Biology
Plant Physiology
Plant Science
Proceedings of the National Academy of Sciences
Science Online
The Scientist
Trends in Biochemical Sciences
Trends in Genetics
Trends in Plant Science
Weed Research
Biological Sciences - Selected Electronic Resources
BioMedNet
Elsevier Trends Journals
WU Libraries Biological or Medical Full-Text Sources
Publishers
Welcome to W. H. Freeman and Co., Publishers
Amazon.com - Query Results
Welcome to Academic Press
Protocols
Sonicated-assisted Agrobacterium-mediated Transformation
Molecular Station (Mol. Biol., Biochem protocols)
Molecular Biology Protocol
Chemistry
Allosteric Effects
Burley Laboratory Home Page
The Biology Project
Welcome to ExPASy
KEGG Encyclopedia
LIGAND Chemical Database for Enzyme Reactions
PRINTS
Chinese
Chinese Character Dictionary
Molecular Biology
Arbeitsgruppe Prof. Dr. Hermann Bujard
BioChemNet Biotechnology
Biological Educational Resources on the Internet
CELL AND MOLECULAR BIOLOGY
Codon Usage Database
DNA Info. & Stock Center, Japan
Emotif exploring the motif universe
Entrez Browser
framesetopenform at www4
Graphics Gallery
IUBio Archive for Biology data and software
METHDS-REAGNTS-bionet.molbio.methds-reagnts N.
MOLECULAR BIOLOGY AND PHYSIOLOGY RESOURCES ON.
PLACE Home
Plant Hormones
Proteome, Inc
RECOMBINATION-bionet.molbio.recombination New.
Robert Martienssen, Cold Spring Harbor Labora.
Technical Tips Online
The National Center for Biotechnology Informa.
Tm Determination
Transposon Annotation
UCDvS Molecular Biology Tools
Stephen C. Winans
biotechnology (Good molecular biology)
Molecular Biology Contents
Microbiology Faculty - The University of Iowa.
Plant Molecular Biology Methods
Molecular Biology Companies
AIMS Combined Searching & Ordering System
Calbiochem Home Page
Dynal AS
Incyte Home Page
Life Technologies, Inc
Yahoo! Finance
Yahoo!
Login to Web Order Entry
Molecular Dynamics Home Page
Fast Gel Electrophoresis
Fast Gel Electro Gel Boxes RAGE
Ambion Incorporated
Institutes
Donald Danforth Plant Science Center
Faculty
Teaching
Graphics Gallery
Molecular Biology Contents
EssentialCellBiology.com
FAOSTAT Database Collections
XVI International Botanical Congress
The Virtual Foliage Home Page!
Images
Plant Image Gallery
Interesting Plants
The Carnivorous Plant FAQ