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RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping¹

Department of Zoology and Genetics (W.Z., S.D.S., V.B.) and Department of Statistics (V.B.), Iowa State University, Ames, Iowa 50011–3260

Expressed sequence tags (ESTs) currently encompass more entries in the public databases than any other form of sequence data. Thus, EST data sets provide a vast resource for gene identification and expression profiling. We have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing. All results of this study were parsed into a database and are accessible via a flexible Web interface at http://www.plantgdb.org/AtGDB/.

¹ This work was supported in part by the National Science Foundation (grant no. DBI–0110254 to V.B.).

^* Corresponding author; e-mail vbrendel{at}iastate.edu; fax 515–294–6755.

Received November 21, 2002; returned for revision January 6, 2003; accepted February 20, 2003.

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