Optimizing PCR primers targeting the bacterial 16S ribosomal ... | 合法醫療器材資訊網

由FSambo著作·2018·被引用31次—Sincethe16Sgenesequenceissimilarbutnotidenticalindifferentorganisms,degenerateprimersareusedfor16SrRNAsequencing.Aprimer ...

As stated in the previous paragraph, an optimal primer-set-pair should simultaneously maximize efficiency and coverage and minimize matching-bias. In the following, we describe how we quantitatively encoded these constraints.

The perfect primer-set-pairs should satisfy several constraints, aimed at improving PCR efficiency and specificity [7]. However, concurrently satisfying all constraints is often impractical and most state-of-the-art primers violate one or more constraints [16]. We thus decided to introduce efficiency as an optimization score, encoding many of the constraints as fuzzy score functions. More precisely, we defined our efficiency score as the sum of ten score terms: seven fuzzy score terms related to single-primer efficiency constraints, averaged across all primers in the primer-set-pairs, plus three score terms related to the effic...