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.
other · Level V
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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.
Medical subject headings
- Algorithms
- DNA Probes
- Expressed Sequence Tags
- Oligonucleotide Array Sequence Analysis
- Oligonucleotides
- Sequence Alignment
- Sequence Analysis, DNA