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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.


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