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

Bioinformatics. 2004 Feb 12;20(3):428-9. doi: 10.1093/bioinformatics/btg434. Epub 2004 Jan 22.

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.

Publication types

  • Evaluation Study

MeSH terms

  • Algorithms*
  • Artifacts
  • 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

Substances

  • DNA Probes
  • Oligonucleotides