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Nucleic Acids Research, 2003, Vol. 31, No. 22 e141
© 2003 Oxford University Press

Article

FELINES: a utility for extracting and examining EST-defined introns and exons

Scott D. Drabenstot, Doris M. Kupfer1, James D. White1, David W. Dyer, Bruce A. Roe1, Kent L. Buchanan2 and Juneann W. Murphy*

Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, PO Box 26901, BMSB 1053, Oklahoma City, OK 73190, USA, 1 Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA and 2 Department of Microbiology and Immunology, Tulane University Medical Center, New Orleans, LA 70112, USA

*To whom correspondence should be addressed. Tel: +1 405 271 6622; Fax: +1 405 271 3117; Email: juneann-murphy{at}ouhsc.edu

FELINES (Finding and Examining Lots of Intron ‘N’ Exon Sequences) is a utility written to automate construction and analysis of high quality intron and exon sequence databases produced from EST (expressed sequence tag) to genomic sequence alignments. We demonstrated the various programs of the FELINES utility by creating intron and exon sequence databases for the fungal organism Schizosaccharomyces pombe from alignments of EST to genomic sequences. In addition, we analyzed our constructed S.pombe sequence databases and the well-established Saccharomyces cerevisiae intron database from Manuel Ares’ Laboratory for conserved sequence motifs. FELINES was shown to be useful for characterizing branchsites, polypyrimidine tracts and 5' and 3' splice sites in the intron databases and exonic splicing enhancers (ESEs) in S.pombe exons. FELINES is available at http://www.genome.ou.edu/informatics.html.


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