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

• Published in: Bioinformatics 2004-02, Vol.20 (3), p.428-429
• Main Authors: Hornshøj, Henrik, Stengaard, Henrik, Panitz, Frank, Bendixen, Christian
• Format: Article
• Language: English
• Subjects: Algorithms; DNA Probes - chemistry; Exons - genetics; Expressed Sequence Tags - chemistry; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotides - chemistry; Oligonucleotides - genetics; Quality Control; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btg434

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/