The integration of quality model to the primer design process with Primer3 software
Name
Maarja Lepamets
Abstract
The success rate of polymerase chain reaction (PCR) is highly dependent on the binding specificity and stability of the primers currently in use. Primers with more binding sites tend to have higher failure rates. In the current study a model for predicting primer failure rates based on the number of their binding sites was fit. Next, the model was used in an algorithm which would mask the regions of a given input sequence that are unsuitable for primer design. The described algorithm was then integrated to Primer3 software where it was tested in the context of primer design. Our results show that by using the masking functionality one can reduce the primer failure rate more than two times.
Graduation Thesis language
Estonian
Graduation Thesis type
Master - Computer Science
Supervisor(s)
Lauris Kaplinski
Defence year
2015