Abstract: High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. HT-SELEX has become the method of choice for the identification of (ribo)nucleic molecules that bind to diverse spectrum of molecular targets. However, HT-SELEX generate vast amount of data demanding new analysis tools. To close this gap, our group has developed a number of HT-SELEX analysis methods. In particular, our AptaCluster algorithm allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets. Next, we utilized our clustering algorithm to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery using our new algorithm AptaMut. Finally, I will present AptaTRACE, a novel approach for the identification of sequence-structure binding motifs in HT-SELEX derived aptamers. Leveraging the experimental design of the SELEX protocol, AptaTRACE identifies sequence-structure motifs that show gradually increasing signature of selection. We will show performance of these techniques on experimental data.
Thursday, March 31, 2016
Host: Remo Rohs