SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures

RNA aptamer selection during SELEX experiments builds on secondary structural diversity. Advanced structural comparison methods can focus this diversity. We develop SICOR, which uses probabilistic subgraph isomorphisms for graph distances between RNA secondary structure graphs. SICOR outperforms other comparison methods and is applicable to many structural comparisons in experimental design.

1 Introduction

RNA aptamers can form a multitude of structures to promote catalytic activity or interaction with different partners such as proteins or small molecules whose affinities and selectivities can rival those of antibodies [1], [2]. Thus aptamers are of ever-increasing interest in science, as they can be used for a variety of applications, e.g., as diagnostic tools, therapeutic agents, or synthetic biosensors in various applications [3], [4].