TaGDB displays high quality spliced alignments for EST, cDNA, PUT, and model species proteins.
More about alignments...
Transcript sequences displayed at TaGDB were aligned to genomic sequence using GeneSeqer, which performs a consensus spliced alignment on ESTs and cDNA, providing both cognate and non-cognate alignments for improved gene prediction (Brendel et al., 2004).
Microarray probes (if any) were matched to the PUT assembly sequence using Vmatch and then coordinately transfered to genomic location.
Search/Download
Search or download any splice-aligned sequences, gene models, or genomic sequence from TaGDB. The entire TaGDB dataset can also be downloaded.
More about search / download...
Search for any TaGDBgene or aligned sequence by ID or keyword, and download complete sequence or flanking 5' or 3' regions, exons, or introns (FASTA format).
For any specified genomic region, download genomic DNA (FASTA format), all aligned/computed transcripts or proteins (FASTA format), or all genome annotations (GenBank, GFF3 or EMBL format).
Download bzip2 files and MySQL tables representing complete TaGDB dataset
Note: sequences displayed here may not reflect the latest Triticum aestivum sequence count at PlantGDB, which can be viewed on our download page.
Tools
Sequence analysis tools accessed from the Genome Context View menu use the current genomic region as input. Or, to access the same tools without a genomic context, use TaGDB left menubar Tools links.
More about tools...
Use BLASTn, BLASTp, tBLASTn and tBLASTx to match a query sequence to TaGDB sequences.
BLAST-able datasets include Triticum aestivum genomic DNA, splice-aligned transcripts and proteins, gene models, and other aligned sequences.
Spliced alignment of user-specified transcript datasets to genomic DNA from any region in TaGDB. User can specify splice site model and stringency level.
Help annotate the Triticum aestivum genome using our yrGATE gene structure annotation tool
(see Overview),
aided by GAEVAL tables that flag problematic gene models.
Video demo: QuickTime
Flash
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Custom Track Display
Distributed Annotation Service (DAS) (see Overview) is available for displaying remotely served genome alignments at TaGDB, as well as for displaying selected TaGDB tracks on a different genome browser (e.g. Ensembl, GBrowse). How to use DAS...
To add a DAS track to TaGDB using our DAS client, first select desired genome coordinates above and click "Go", then select menu item "Configure -> Add Track" and paste in the appropriate DAS URL.
To view TaGDB tracks in another genome browser (e.g. Ensembl, Gbrowse) using our DAS server, first find the appropriate xDAS Server URL on our DAS overview page, then follow instructions on the remote browser website for adding the remote track. NOTE: DAS service available for certain tracks only.
For more details, refer to DAS section in our Genome Browser help pages.
Additional custom track display features are under development.
Annotated protein alignments
Annotated Protein Alignments: A searchable table of splice-aligned, annotated protein models. TBD.
Support
Genome browser video demo: QuickTime
Flash For help pages and tutorials focusing on genome browser features and gene annotation, see side bar.
