Skip Navigation



Nucleic Acids Research Advance Access published online on April 16, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm220
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2757K) Freely available
Right arrow Screen PDF (576K) Freely available
Right arrow Supplementary Material
Right arrowOA All Versions of this Article:
35/suppl_2/W148    most recent
gkm220v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Mitchell, R. A. C.
Right arrow Articles by Rawlings, C. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Mitchell, R. A. C.
Right arrow Articles by Rawlings, C. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Paper

Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence

Rowan A. C. Mitchell1,*, Nathalie Castells-Brooke1, Jan Taubert1, Paul J. Verrier1, David J. Leader2,3 and Christopher J. Rawlings1

1Biomathematics and Bioinformatics Division and 2Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK

*To whom correspondence should be addressed. Tel: +44 (0)1582 763133; Fax: +44 (0)1582 763010; Email: rowan.mitchell{at}bbsrc.ac.uk

Received January 29, 2007. Revised March 23, 2007. Accepted March 28, 2007.

Wheat biologists face particular problems because of the lack of genomic sequence and the three homoeologous genomes which give rise to three very similar forms for many transcripts. However, over 1.3 million available public-domain Triticeae ESTs (of which ~850 000 are wheat) and the full rice genomic sequence can be used to estimate likely transcript sequences present in any wheat cDNA sample to which PCR primers may then be designed. Wheat Estimated Transcript Server (WhETS) is designed to do this in a convenient form, and to provide information on the number of matching EST and high quality cDNA (hq-cDNA) sequences, tissue distribution and likely intron position inferred from rice. Triticeae EST and hq-cDNA sequences are mapped onto rice loci and stored in a database. The user selects a rice locus (directly or via Arabidopsis) and the matching Triticeae sequences are assembled according to user-defined filter and stringency settings. Assembly is achieved initially with the CAP3 program and then with a single nucleotide polymorphism (SNP)-analysis algorithm designed to separate homoeologues. Alignment of the resulting contigs and singlets against the rice template sequence is then displayed. Sequences and assembly details are available for download in fasta and ace formats, respectively. WhETS is accessible at http://www4.rothamsted.bbsrc.ac.uk/whets.

3Pressent address: David J. Leader, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J Exp BotHome page
D. Z. Habash, Z. Kehel, and M. Nachit
Genomic approaches for designing durum wheat ready for climate change with a focus on drought
J. Exp. Bot., July 1, 2009; 60(10): 2805 - 2815.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. Mochida, T. Yoshida, T. Sakurai, Y. Ogihara, and K. Shinozaki
TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics
Plant Physiology, July 1, 2009; 150(3): 1135 - 1146.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.