Supported by the HFSP and the NSF/NIGMS


Our RNA-As-Graph-Pools (RAGPOOLS) aims to engineer structured pools and examine pool properties for in vitro selection of RNAs and related problems. We develop an approach for engineering sequence pools that links RNA sequence space regions with corresponding structural distributions via a "mixing matrix" approach combined with a graph theory analysis. In constrast to random pools, which are associated only with a local region of sequence space, our designed pools target specific motifs, which could increase the probability of discovering novel RNAs. Experimental synthesis of designed pools can benefit from using optimized starting sequences, mixing matrices, and pool fraction associated with each of our constructed mixing matrix as a guide.

Use the RNA Pool Design tutorials to learn about useful topics that will help you use our RNA-As-Graph-Pools (RAGPOOLS). The tutorial topics include brief explanations of in vitro selection, modeling of pool synthesis (mixing matrix, starting sequences, and optimization algorithm), and use of web-based design.

RNA Pool Designer RNA Pool Designer can help to improve in vitro selection by optimizing the mixing matrix generators for a given target structure.

RNA Pool Analyzer RNA Pool Analyzer will analyze a given starting sequence.

1. Kim N, Shin JS, Elmetwaly S, Gan HH, and Schlick T. RAGPOOLS:RNA-As-Graph-Pools - A web server for assisting the design of structured RNA pools for in vitro selection. (2007) In press in Bioinformatics. Download PDF

2. Kim N, Gan HH, and Schlick T. A computational proposal for designing structured RNA pools for in vitro selection of RNAs. (2007) RNA 13, 478-92.

Last updated: August 20 2007