OligoSpecificitySystem: global matching efficiency calculation of oligonucleotide sets taking into account degeneracy and mismatch possibilities. (1st January 2014)

• Record Type: Journal Article
• Authors: Michelland, R.J.; Combes, S.; Cauquil, L.
• Is Part Of: International journal of data mining and bioinformatics. Volume 9:Number 4(2014)
• Page Start: 417
• Page End: 423
• Publication Date: 2014-01-01
• Subjects: oligonucleotide -- specificity -- degeneracy -- mismatch -- polymerase chain reaction -- PCR -- hybridisation; Data mining -- Periodicals; Bioinformatics -- Periodicals; 006.312
• Languages: English
• ISSNs: 1748-5673

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.