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Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.

Applications Note

SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments

Henrik Hornshøj *, Henrik Stengaard , Frank Panitz and Christian Bendixen

Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark

Received on March 21, 2003 ; revised on June 10, 2003 ; accepted on August 8, 2003
Advance Access Publication January 22, 2004

Summary: SEPON, Selection and Evaluation Pipeline for OligoNucleotide generates n-mer oligonucleotide sequences from expressed sequence tags of non-annotated genomes for microarray gene-expression profiling. A non-target melting temperature (Tm) algorithm will reduce cross-hybridization by estimating Tm of oligonucleotide hybridization to non-specific targets (non-target Tm) and discard oligonucleotides with non-target Tm estimate above user-defined threshold. SEPON allows user-defined filtering, predicts exon location, assigns penalty based on 3' distance, GC content, secondary structure Tm and non-target Tm and ranks oligonucleotides for optimal selection.

Availability: The program is freely available for non-commercial and academic use under the GNU General Public License and is obtained upon request to authors.

Supplementary information: http://www.agrsci.dk/hag/sepon/

Contact: henrikh.jensen{at}agrsci.dk

* To whom correspondence should be addressed.


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