An ALE-Index Based Algorithm Facilitated Prediction of Success for Polymerase Chain Reactions

Abstract

Polymerase chain reaction (PCR), though invented over twenty years ago and having been developed with much advance, still face challenges nowadays. Long DNA and most high GC content DNA sequences are still hard to amplify. People have had few tools to predict whether a PCR is successful or not before a real PCR experiment is done. In this study, 189 randomly selected short amplicons from human genome were represented as "four horizontal lines" DNA graphs followed by ALE-index based algorithm to compare relative similarities among each other, and were classified as two groups, which basically coincided with the real experimental results in which these amplicons were divided into successful and unsuccessful groups. The accuracy of the algorithm was about 91%.

Prediction of success for polymerase chain reactions using the Markov maximal order model and support vector machine

“…The dataset used in this study is taken from Zhang et al (2009), which contains 189 exons in human chromosomes used as target amplicons. For convenience, we name the dataset Z189.…”

“…The GC contents of the expected amplicons are 32-78%. The experimental procedure of PCR was described in detail in Zhang et al (2009). According to the experimental results, 94 amplicons were marked as "S" which signifies that the PCR reaction was successful, while 95 ones were marked as "U" which signifies that the PCR reaction was unsuccessful (see Table 1).…”

“…In fact, during these years, the experimental procedure of PCR was always the focus of attention, while much less attention was paid to the analysis of the PCR template, the PCR experimental subject itself (Zhang et al, 2009). The most commonly used parameters that relate to a DNA template are only the PCR product size and the melting temperature (T m ) of the product (Zhang et al, 2009;Rychlik, 1993;Rychlik et al, 1990;Rozen and Skaletsky, 2000). Please don't forget that the primer sequence can be modified by biologists, but the target DNA cannot.…”

“…But these endeavors, including the design of primers which was viewed as the crucial to the success of PCR (Innis and Gelfand, 1990;Varadaraj and Skinner, 1994;Haas et al, 1998), are apparently not able to guarantee the success of PCR reactions. In fact, during these years, the experimental procedure of PCR was always the focus of attention, while much less attention was paid to the analysis of the PCR template, the PCR experimental subject itself (Zhang et al, 2009). The most commonly used parameters that relate to a DNA template are only the PCR product size and the melting temperature (T m ) of the product (Zhang et al, 2009;Rychlik, 1993;Rychlik et al, 1990;Rozen and Skaletsky, 2000).…”