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
Open Access
- 22 January 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 20 (3) , 428-429
- https://doi.org/10.1093/bioinformatics/btg434
Abstract
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/Keywords
This publication has 0 references indexed in Scilit: