http://www.arabidopsis.org
The Arabidopsis Information Resource (TAIR) provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. TAIR consists of a searchable relational database, which includes many different datatypes. The data can be viewed using our interactive MapViewer, and analyzed with our tools. Our datasets can also be downloaded for your convenience. In addition, pages on news, information on the Arabidopsis Genome Initiative (AGI), Arabidopsis lab protocols, and useful links are provided.
TAIR is a collaboration between the Carnegie Institution of Washington Department of Plant Biology, Stanford, California, and the National Center for Genome Resources (NCGR), Santa Fe, New Mexico.

http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm
The Arabidopsis Biological Resource Center (ABRC) was established at The Ohio State University in September, 1991. Primary support of the ABRC is from a National Science Foundation grant. Dr. Randy Scholl is the Director of the Center. The mission of the ABRC is to provide collection, preservation and distribution of seeds, and DNA clone and library storage and DNA clone distribution services. The ABRC database functions and ordering system are incorporated into TAIR.
The ABRC's holdings and stock distribution rates have increased rapidly so that presently thousands of stocks are available and more than 70,000 stocks are shipped annually to researchers around the world. Stocks have been shipped to more than 50 countries. Modest user fees are charged, with the exception of small orders from occasional users.
The TAIR database allows users to obtain information about Arabidopsis and order stocks. Stock searches can be conducted, with full stock information being displayed.

http://www.ncgr.org/
In collaboration with users worldwide, NCGR creates biological databases and analytical tools to accelerate and enable discovery. Primary research areas include genomics, biochemical pathways and gene expression.

http://signal.salk.edu/
http://signal.salk.edu/tabout.html
A Sequence-Indexed Library of Insertion Mutations in the Arabidopsis Genome
The Salk Institute Genome Analysis Laboratory (SIGnAL) uses high-throughput genome sequencing methods to identify the sites of insertion of Agrobacterium T-DNA in the Arabidopsis genome. T-DNA transformed plants from the Alonso/Crosby/Ecker collection is grown, genomic DNA is prepared, T-DNA flanking plant DNA is recovered and sequenced. Insertion site sequences are then aligned with the Arabidopsis genome sequence and gene annotation is added when appropriate. The data is available via a web accessible graphical interface-T-DNAExpress- (http://signal.salk.edu/cgi-bin/tdnaexpress) that provides both text and DNA searches of the insertion sequence database. All DNA sequences are deposited into GenBank and provided to The Arabidopsis Information Resource (TAIR). Seeds from the T-DNA insertion lines are deposited with the Arabidopsis Biological Resource Center (ABRC) at Ohio State University, where they propagate and distribute seeds to the community.

http://atarrays.tigr.org/
A significant challenge in all genome projects is the identification and annotation of the genes and the roles they play in development, disease, and response to environmental stresses.
In Arabidopsis, genome sequencing has allowed the identification of approximately 25,500 predicted coding sequences, but significant work remains to provide functional annotation for these. The goal at TIGR is to provide experimental validation for these gene predictions and to begin to assign functional roles to genes using DNA microarray technology as a key tool.
TIGR has a well annotated rice sequence also linked to through our rice family trees. TIGR Maize (Zea mays) Gene Index (ZmGI) is a very good source of sequence for the maize genome currently being sequenced.

http://mips.gsf.de/projects/plants
The MIPS Arabidopsis thaliana Database MAtDB
Arabidopsis thaliana is the first plant for which the complete genome has been sequenced. In order to put the wealth of information represented by the complete genome sequence to use, we must learn to decode this information and to connect it to diverse biological data. A list of all genes of an organism is no more than a list of parts; we need to discover their functions and interactions in order to understand the workings of the whole. The MIPS Arabidopsis thaliana database (MAtDB) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project, part of the Arabidopsis Genome Initiative, but is moving towards becoming an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities. The aim is to create a comprehensive resource for Arabidopsis as a model that can then be used to transfer knowledge onto sequences from other species, including crop plants.

http://cellwall.stanford.edu/
When at Stanford, Todd Richmond developed a resource for plant cell wall biologists, especially those interested in polysaccharide biosynthesis, to collect and organize sequences for several gene families related to plant cell wall biosynthesis. There are four major sections to the site, and two of them focus on the CESA and CSL Superfamily and callose synthases.

http://bioweb.ucr.edu/Cellwall/
Cell Wall Navigator (CWN) is an integrated database and mining tool for protein families involved in plant cell wall metabolism.

 

http://128.192.9.30/web/specdb/ms/pmaa/pframe.html
This site contains a very useful EIMS spectral database for partially methylated alditol acetates (see also our techniques section)

http://www.bio.psu.edu/expansins/
Expansins are a group of extracellular proteins that directly modify the mechanical properties of plant cell walls, leading to turgor-driven cell extension. Within the completely sequenced Arabidopsis genome, Dan Cosgrove’s group has identified 38 expansin sequences that fall into three discrete subfamilies. Check out this site for many aspects of the roles expansin play in plant growth and development.

Gramene is an excellent resource for grass comparative genomics. Their site has extensive information on rice, maize, wheat, barely and other grasses. When you click on the gramene link button in our rice gene trees you will be taken to their genome browser displaying gene, marker, EST, and BAC information as well as synteny between grass species. Many elements are clickable for further information.

OryGenes has collected data from rice knockout lines such as Tos17, T-DNA, and Ds lines. This is a good resource to look at for available knockouts of genes in rice and is linked through our rice family trees to search a particular gene for available knockouts.

Multalin at the LBMGE Genomics ToolBox is an online program available to align multiple gene sequences. This is a very useful tool to look at gene families for common sequence stretches and to look for homology of genes in gene families from different species.

ClustalW is a very good program to look at family relationships of genes. Sequence data can be input to this site at the Kyoto University Bioinfomatics Center and a family tree structure retrieved for use in tree drawing programs.

TreeDyn is a very powerful downloadable phylogenetic program that can use the output from ClustalW or another tree file generating program to create, edit, and annotate trees. We use this program to generate the trees shown in the gene families section.