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 |
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Authors: | Hornshøj Henrik Stengaard Henrik Panitz Frank Bendixen Christian |
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Institution: | Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark. henrikh.jensen@agrsci.dk |
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Abstract: | 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 (T(m)) algorithm will reduce cross-hybridization by estimating T(m) of oligonucleotide hybridization to non-specific targets (non-target T(m)) and discard oligonucleotides with non-target T(m) estimate above user-defined threshold. SEPON allows user-defined filtering, predicts exon location, assigns penalty based on 3' distance, GC content, secondary structure T(m) and non-target T(m) and ranks oligonucleotides for optimal selection. |
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