Title: OligoSpecificitySystem: global matching efficiency calculation of oligonucleotide sets taking into account degeneracy and mismatch possibilities

Authors: R.J. Michelland; S. Combes; L. Cauquil

Addresses: INRA, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31326 Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31326 Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31076 Toulouse, France. ' INRA, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31326 Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31326 Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31076 Toulouse, France. ' INRA, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31326 Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31326 Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31076 Toulouse, France.

Abstract: Oligonucleotide sets are widely used in molecular biology to target a group of nucleic acid sequences using Polymerase Chain Reaction (PCR)-based technologies. Currently, the global matching efficiency of an oligonucleotide set is considered to be equal to the lower matching efficiency calculated for each oligonucleotide. However, sequences matching the limiting oligonucleotide did not always match the other oligonucleotide of the set, resulting in a biased evaluation of the matching efficiency. The Oligo- SpecificitySystem program avoid this bias by calculations of the real global matching efficiency of oligonucleotide sets. It can process all kinds of oligonucleotide sets, including the number of oligonucleotides, base pair degeneracy occurrences or mismatch occurrences.

Keywords: oligonucleotide sets; specificity; base pair degeneracy; mismatch; polymerase chain reaction; PCR; hybridisation; bioinformatics; nucleic acid sequences; matching efficiency; molecular biology.

DOI: 10.1504/IJDMB.2014.062148

International Journal of Data Mining and Bioinformatics, 2014 Vol.9 No.4, pp.417 - 423

Received: 31 May 2010
Accepted: 16 Jun 2011
Published online: 21 Oct 2014 *

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