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Bioinformatics Advance Access published online on January 22, 2004
Bioinformatics, doi:10.1093/bioinformatics/btg434
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received March 21, 2003
Revised June 10, 2003
Accepted August 8, 2003

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 Jensen 1*, Henrik Stengaard 1, Frank Panitz 1, Christian Bendixen 1

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

* To whom correspondence should be addressed. E-mail: henrikh.jensen{at}agrsci.dk.


  Abstract

Summary: SEPON generates n-mer oligonucleotide sequences from Expressed Sequence Tags (ESTs) 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/


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