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

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%.