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

Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Carnegie Institution, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA. dswarbreck@stanford.edu

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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Related in: MedlinePlus

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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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.

Mentions: As the variety and extent of data mapped to the Arabidopsis genome continues to increase there is a greater need to visualize genomic annotation and features from multiple sources in a single viewer. To facilitate this, we have recently added the popular genome viewer GBrowse (1). TAIR GBrowse (Figure 1) expands upon the capabilities of the pre-existing TAIR genome viewer (SeqViewer), offering the community a highly configurable display for viewing genomic annotations. GBrowse can be accessed from the Tools menu or TAIR detail pages (e.g. Locus and Polymorphism pages). A variety of annotation tracks are provided including gene models and their supporting transcript evidence as well as markers, clones, T-DNA and transposon insertions and polymorphisms. A track showing percent similarity between aligned Arabidopsis and Populus trichocarpa genomic sequences is provided through the VISTA plugin (2). Other datasets to be added to GBrowse in the near future include cross-species transcript alignments, additional genomic conservation tracks, endogenous transposable elements, expression data (e.g. SAGE) and methylation data. Additionally, users can upload their own annotation data into GBrowse from a local text file, allowing them to view private annotations in the context of existing public data.Figure 1.


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

Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E - Nucleic Acids Res. (2007)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238962&req=5

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.
Mentions: As the variety and extent of data mapped to the Arabidopsis genome continues to increase there is a greater need to visualize genomic annotation and features from multiple sources in a single viewer. To facilitate this, we have recently added the popular genome viewer GBrowse (1). TAIR GBrowse (Figure 1) expands upon the capabilities of the pre-existing TAIR genome viewer (SeqViewer), offering the community a highly configurable display for viewing genomic annotations. GBrowse can be accessed from the Tools menu or TAIR detail pages (e.g. Locus and Polymorphism pages). A variety of annotation tracks are provided including gene models and their supporting transcript evidence as well as markers, clones, T-DNA and transposon insertions and polymorphisms. A track showing percent similarity between aligned Arabidopsis and Populus trichocarpa genomic sequences is provided through the VISTA plugin (2). Other datasets to be added to GBrowse in the near future include cross-species transcript alignments, additional genomic conservation tracks, endogenous transposable elements, expression data (e.g. SAGE) and methylation data. Additionally, users can upload their own annotation data into GBrowse from a local text file, allowing them to view private annotations in the context of existing public data.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Carnegie Institution, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA. dswarbreck@stanford.edu

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.

Show MeSH
Related in: MedlinePlus