The Arabidopsis Information Resource (TAIR): gene structure and function annotation

Abstract

The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research community. New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007. A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models). A total of 681 new genes and 1002 new splice variants were added. Overall, 10 098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release.

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

“…Summary of EST, cDNA, and Reported ncRNA Data Sets TAIR9 annotation files (Swarbreck et al, 2008) were downloaded from the FTP server of TAIR (ftp://ftp.Arabidopsis.org/), and the sequences and genomic loci of 350 "other RNAs" were parsed from the gff-formatted file. The National Center for Biotechnology Information UniGene database build 73 contains 1,045,472 Arabidopsis EST or cDNA sequences.…”

The new FioreDB database provides comprehensive information on plant transcription factors and phenotypes induced by CRES-T in ornamental and model plants

“…All sequence data (coding sequences and genomic sequences) for Arabidopsis thaliana that is stored in FioreDB was downloaded from TAIR (TAIR9) (http://www.arabidopsis.org/, Swarbreck et al 2008). Gene sequences and their flanking regions were excised from the genome sequence using an original Perl script (http://www.perl.org/).…”

“…The information from TAIR (Swarbreck et al 2008) includes the gene alias and description, the gene ontology classification, the gene model, sequences of the coding regions, the amino acid sequences, and the genomic sequences around the genes. In addition, information from the Arabidopsis Small RNA Project (ASRP) (Backman et al 2008) for miRNAs/tasiRNAs is provided if the gene is targeted by them.…”

“…The new FioreDB is available through a simple web-based interface that provides easy access to information about TFs that induce phenotype of interest by applying CRES-T. FioreDB also provides information on TF classification based on our original criteria along with details of the transcriptional repression domain found in Arabidopsis proteins including proteins that are not TFs. In addition, FioreDB contains information on all Arabidopsis genes, including sequences and microarray data from the Arabidopsis Information Resource (TAIR) (http://www.arabidopsis.org/, Swarbreck et al 2008) and other web sites. The new FioreDB will contribute to basic research of plant TFs and to the manipulation of traits of agronomically important plants using CRES-T, especially from the point of view of horticulture.…”

InterOnto – Ranking Inter-Ontology Links

“…Consider for instance the Arabidopsis Information Resource (TAIR) [20]. In TAIR genes are annotated with concepts from the Gene Ontology (GO) [1] and the Plant Ontology (PO) [7].…”