The Arabidopsis Information Resource (TAIR)
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TAIR is the model organism database for Arabidopsis thaliana. |
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Contents
About The Arabidopsis Information Resource (TAIR)
The Arabidopsis Information Resource (TAIR) is the model organism database for Arabidopsis thaliana, providing integration of the available genomic data from the Arabidopsis community at large, as well as published literature and genome centers.
Content
TAIR encompasses information on the Arabidopsis genome with information on the genes, markers, polymorphisms, maps, sequences, clones, DNA, seed stocks, gene proteins and families, genome-wide expression data and biochemical pathways, as well as publications
Using The Arabidopsis Information Resource (TAIR)
Browsing
Browsing TAIR is like any other site. There are plenty of links on the front page to direct the user's attention. The page header has the following categories: Advanced Search, Analysis Tools, Portals, FTP Downloads, Arabidopsis Information and Stocks. Each of these headings has a substantial number of sub-headings.
Searching
Searching TAIR seems to be straight-forward. There are two options for searching: either using the search bar on the main page, or clicking to the advanced search page.
There are several directions that one can search. For example, if one wanted to find information based on the gene Ku70, typing in Ku70 in the search bar and selecting Gene would pull-out the information on Ku70. Giving information on the Locus, gene model, a description of the gene, the full-length cDNA and keywords that are related to its Gene Ontology Description. Clicking on the Locus link pulls up the full page on the locus, including the ATG number, other names, the GO Annotations, any available RNA Data, Associated transcripts, the Chromosome it is located on and any predicted protein data (AA, Mw, IP,predicted domains).
There are additional, standard searches that can be done: searching by vector, sequences, microarray, and polymorphism/alleles.
Another nice search feature included in TAIR is the ability to search the Arabidopsis community by PI or lab. Searching for a researcher in the Arabidopsis field, if they are a registered user of TAIR, will pull-up the person's contact information, publications and affiliations. This is particularly nice because one can check a particular paper and see the annotations for the identified genes in that publication.
Usage examples
Add links to additional pages describing success stories here.
Technology
The TAIR website employs several tools for visualization, sequence analysis and data retrieval.
- MapViewer: MapViewer is a graphical interface for the integration of genetic, physical and sequence-based maps for each chromosome.
- SeqViewer is the viewer for displaying gene annotation, clones, markers, transcripts and polymorphisms on the genome.
- BLAST tools are available at the site for searching against a variety of datasets.
- FASTA for searching against a variety of datasets.
- PatMatch was designed to identify short nucleotide and amino acid motifs using regular expressions for searching.
- Bulk data retrieval allows users to retrieve large numbers of data.
- Ordering Stocks is made easy with the collaboration with ABRC for the searching and ordering of stocks and strains from TAIR.
Web Services/API
Discussion
References
See Help:References for how to manage references in EcoliWiki.
TAIR: a resource for integrated Arabidoposis data
Garcia-Hernandez et. al Functional Integrated Genomics (2002) 2:239-253 Abstract Full-Text
External Links
The Arabidopsis Information Resource (TAIR)
