Sequence Dependence of Isothermal DNA Amplification via EXPAR
Jifeng Qian, PhD Candidate, will discuss the Niemz Lab’s work on developing a computational tool for sequence dependence of EXPAR (exponential amplification reaction) templates. In the isothermal EXponential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently in the reaction. Two computational methods are developed to predict EXPAR template performance based on sequence: a position weight matrix approach combined with a support vector machine based classifier, and RELIEF attribute evaluation combined with Naïve Bayes machine learning. Using either method, approximately 67-70% sensitivity and approximately 77-80% specificity can be achieved between well versus poorly performing EXPAR templates. This computational tools can significantly accelerate new EXPAR assay design as well as provide fundamental insights about unconventional polymerase activity that may be involved in non-specific amplification in EXPAR and other nucleic acid amplification reactions.
Please RSVP to Lindsay Janssen if you plan to attend.
Lunch will be provided.
|Where:||KGI Main Campus, Building 535, 152 Classroom|
|When:||November 9, 2011, 12:00 p.m. - 1:00 p.m.|