The Arabidopsis Information Resource (TAIR): gene structure and function annotation - PubMed (original) (raw)

. 2008 Jan;36(Database issue):D1009-14.

doi: 10.1093/nar/gkm965. Epub 2007 Nov 5.

Christopher Wilks, Philippe Lamesch, Tanya Z Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang, Eva Huala

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

David Swarbreck et al. Nucleic Acids Res. 2008 Jan.

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.

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Figures

Figure 1.

Figure 1.

TAIR GBrowse. The TAIR GBrowse tool allows navigation of the five A. thaliana nuclear chromosomes plus the mitochondrial and chloroplast genomes. A 10 kb region including AT4G39680 and AT4G39690 is shown (coding regions in dark blue and UTRs in light blue). Selected tracks shown here include cDNAs (dark green), ESTs (light green for forward orientation and light brown for reverse), T-DNA and transposon insertions (orange triangles), polymorphisms (yellow diamonds) and the VISTA plot showing sequence similarity with poplar. Additional tracks (data not shown) include CDS segments, markers and GC content. All elements shown in GBrowse can be clicked on to access the TAIR detail page for that object.

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