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|Switchgrass Functional Genomics Server|
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PviUTs (uniqe transcript sequences)
Download switchgrass rna-seq data
This web server provides restricted access to assembled switchgrass (Panicum virgatum L.) unique transcript sequences (PviUTs), a gene expression atlas (PviGEA), GBrowser views of ESTs mapped to the PviUTs, and other data.
Currently, PviUT version 1.2 is a low-redundancy collection of unitranscript sequences of Alamo-AP13 (AP13), Alamo (non-AP13, Alam), Kanlow (Kanl), Summer-VS16 (VS16), and other pooled genotypes (Oths), which were assembled with Newbler (454-ESTs) and PAVE (Sanger-ESTs or Sanger-ESTs plus Newbler-assemblies of 454-ESTs).
Current search and download options on the unitranscript (PviUTs) page include: a keyword search, which enables queries and downloads of all sequences annotated with a particular function (e.g. "ABC transporter"); BLAST search, which enables queries with a reference sequence(s) that yield a list of homologous sequences in the database; and unitranscript ID search, which enables downloads of sequences from a list of unitranscript identifiers.
On the switchgrass gene expression atlas (PviGEA) page, probeset ID and PviUT ID can be used to search for specific gene expression profiles. A BLAST search function will be available as soon as probe sequences and probe targets are posted.
Funding Support and ContactThis work is part of a project to develop tools for switchgrass functional genomics that is funded by the BioEnergy Science Center (BESC). BESC is a US Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. For questions, please contact the principle investigator, For questions regarding the web server, please contact site administrator.
CitationZhang, J., Lee, Y., Torres-Jerez, I., Wang, M., Yin, Y., Chou, W-C., He, J., Shen, H., Srivastava, A. C., Pennacchio, C., Lindquist, E., Grimwood, J., Schmutz, J., Xu, Y., Sharma, M., Sharma, R., Bartley, L.E., Ronald, P., Saha, M. C., Dixon, A., Tang, Y. & Udvardi, M. K. (2013). Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). Plant Journal, January, doi:10.1111/tpj.12104.
News & Service Updates[2014/05/01] Data for 7 time points of seed development were included in the gene expression atlas.
[2011/07/15] A gene expression atlas with 14 major switchgrass plant tissues/organs was established.
[2011/07/8] A GBrower view of ESTs mapped to the PviUTs was created and linked to the IDs.
[2011/01/26] The low-redundancy switchgrass unitranscript sequence data and functional annotation were deposited.
[2010/06/30] Assemblies of Alamo-AP13 ESTs using different strategies, programs.and combinations were deposited for manual evaluation.
[2009/03/01] Assembled ESTs of Summer VS16 were deposited. Server name changed to "Switchgrass EST Server".
[2008/10/20] First Version Announced: We are pleased to announce the first version of our switchgrass EST project support server.
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