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

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 OligoSpecificitySystem 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.