Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (581K) Freely available
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 ISI Web of Science
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 Search for citing articles in:
ISI Web of Science (23)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Schlueter, S. D.
Right arrow Articles by Brendel, V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schlueter, S. D.
Right arrow Articles by Brendel, V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 13 3597-3600
© 2003 Oxford University Press

GeneSeqer@PlantGDB: gene structure prediction in plant genomes

Shannon D. Schlueter1, Qunfeng Dong1 and Volker Brendel*,1,2

1 Department of Zoology and Genetics, Iowa State University, Ames, IA 50011-3260, USA 2 Department of Statistics, Iowa State University, Ames, IA 50011-3260, USA

*To whom correspondence should be addressed. Tel: +1 5152949884; Fax: +1 5152946755; Email: vbrendel{at}iastate.edu

The GeneSeqer@PlantGDB Web server (http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi) provides a gene structure prediction tool tailored for applications to plant genomic sequences. Predictions are based on spliced alignment with source-native ESTs and full-length cDNAs or non-native probes derived from putative homologous genes. The tool is illustrated with applications to refinement of current gene structure annotation and de novo annotation of draft genomic sequences. The service should facilitate expert annotation as a community effort by providing convenient access to all public plant sequences via the PlantGDB database, a simple four-step protocol for spliced alignment and visually appealing displays of the predicted gene structures in addition to detailed sequence alignments.


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
 Plant Physiol.Home page
B. A. Kronmiller and R. P. Wise
Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize
Plant Physiology, October 1, 2009; 151(2): 483 - 495.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Liang, L. Liu, and G. Ji
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W77 - W83.
[Abstract] [Full Text] [PDF]

Home page
 Mol PlantHome page
C. Fan, Y. Zhang, Y. Yu, S. Rounsley, M. Long, and R. A. Wing
The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice
Mol Plant, September 1, 2008; 1(5): 839 - 850.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
J. A. Schlueter, B. E. Scheffler, S. Jackson, and R. C. Shoemaker
Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana
J. Hered., March 2, 2008; (2008) esn010v1.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
J. A. Schlueter, I. F. Vasylenko-Sanders, S. Deshpande, J. Yi, M. Siegfried, B. A. Roe, S. D. Schlueter, B. E. Scheffler, and R. C. Shoemaker
The FAD2 Gene Family of Soybean:: Insights into the Structural and Functional Divergence of a Paleopolyploid Genome
Crop Sci., January 1, 2007; 47(Supplement_1): S-14 - S-26.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. A. Schlueter, B. E. Scheffler, S. D. Schlueter, and R. C. Shoemaker
Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.)
Genetics, October 1, 2006; 174(2): 1017 - 1028.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Lomsadze, V. Ter-Hovhannisyan, Y. O. Chernoff, and M. Borodovsky
Gene identification in novel eukaryotic genomes by self-training algorithm
Nucleic Acids Res., November 28, 2005; 33(20): 6494 - 6506.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
Q. Dong, C. J. Lawrence, S. D. Schlueter, M. D. Wilkerson, S. Kurtz, C. Lushbough, and V. Brendel
Comparative Plant Genomics Resources at PlantGDB
Plant Physiology, October 1, 2005; 139(2): 610 - 618.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. D. Wu and C. K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics, May 1, 2005; 21(9): 1859 - 1875.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Q. Dong, S. D. Schlueter, and V. Brendel
PlantGDB, plant genome database and analysis tools
Nucleic Acids Res., January 1, 2004; 32(90001): D354 - 359.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. J. Lawrence, Q. Dong, M. L. Polacco, T. E. Seigfried, and V. Brendel
MaizeGDB, the community database for maize genetics and genomics
Nucleic Acids Res., January 1, 2004; 32(90001): D393 - 397.
[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.